Medical Bookkeeping for Australian Doctors and Practices
Medicare deposits land in one lump. HICAPS settles net of fees. Your contractor doctors want their statements by Friday, and the BAS needs every insurer report split out from the GST-free consults. Medical bookkeeping is the work that ties all of it back to what your practice system billed, every month, inside your own Xero or MYOB file. We offer fixed-fee plans with monthly pricing.
What Does a Medical Bookkeeper Do for a GP Practice in Australia?
A medical bookkeeper keeps the practice ledger matched to what was actually billed: Medicare and patient receipts, practitioner payments, payroll, supplier bills and the GST coding behind the BAS. It is the same discipline as any outsourced bookkeeping engagement, with four income streams that settle on different days. Bookkeeping for doctors is not medical billing: claiming and item coding stay with your practice team, and we start where the money lands.
Medicare and Patient Receipts
Bulk billed Medicare benefits, DVA claims, card payments through Tyro and private health fund rebates through HICAPS each arrive as batched deposits, usually net of fees. We match every deposit to the billing report from your practice system, record the fees as a cost, and chase the gaps before month end.
Practitioner Payments
Employed doctors go through payroll. Contractor doctors on a service fee arrangement need a statement showing gross billings, the fee the practice retained and the net amount paid. We build that statement every pay cycle, so each doctor sees exactly the numbers the ledger holds.
Payroll and Superannuation
Reception, nursing and practice management staff are paid under the award your practice applies, reported through Single Touch Payroll, with super calculated on every pay run. Where you want payroll handled end to end, it runs as its own engagement alongside the books.
GST Coding and BAS Preparation
Every income line is coded GST-free or taxable when it is recorded, not sorted at quarter end. We prepare the BAS figures and the reconciliation behind them, so your registered agent reviews a finished file and lodges it rather than rebuilding the quarter.
Monthly Practice Reports
A profit and loss, balance sheet and cash position every month, plus billings and fees by practitioner and by site. Medical practice financial management then runs on this month’s numbers instead of last year’s tax return, which is when most owners first see a problem.
How Much Does Medical Bookkeeping Cost in Australia for a GP Clinic or Medical Practice?
Most Australian GP clinics pay between AUD 250 and AUD 2,100 a month plus GST for medical practice bookkeeping. Where you land depends on the number of doctors, how many payment streams need reconciling, and whether payroll, practitioner statements and BAS preparation sit inside the fee. Price the employee alternative before you compare one quote with another.
What Australian Firms Publish
Published prices from Australian medical bookkeeping firms, checked on 20 October 2026, run from AUD 250 a month for bookkeeping alone, with BAS preparation from AUD 150 and payroll charged per payslip, through AUD 400 a month for a bundled bookkeeping and BAS plan, to AUD 1,200 plus GST for a clinic with one to four GPs and AUD 2,100 plus GST for five to fifteen. The gap is scope, not skill. A fee that leaves out practitioner statements or the HICAPS reconciliation moves that work back onto your practice manager.
What an In-House Bookkeeper Costs
Jobs and Skills Australia puts median full-time earnings for bookkeepers at AUD 1,400 a week, across 91,800 people in the occupation. That is AUD 72,800 a year. Add the superannuation guarantee at 12 per cent, AUD 8,736, and one bookkeeper costs AUD 81,536 before payroll tax, workers compensation, leave cover, software or the recruitment fee when they resign. That works out to roughly AUD 6,795 a month for one person whose work still needs a second set of eyes.
| Cost line | One in-house bookkeeper | GATP Solutions |
|---|---|---|
| Base salary at the median | AUD 72,800 a year | One fixed monthly fee |
| Superannuation guarantee at 12 per cent | AUD 8,736 a year | Included |
| Subtotal | AUD 81,536 a year | Fixed fee, scoped to your volume |
| Payroll tax and workers compensation | Apply on top of wages | Included |
| Cover during annual leave | The reconciliation stops | Team coverage |
| Review of the work | A second person needed | Built into the team |
Should a Medical Practice in Australia Outsource Its Bookkeeping or Hire an In-House Bookkeeper?
Outsource while the bookkeeping fits inside one or two days a week and your practice manager can approve rather than chase. Hire when the volume is a full-time job on its own, which usually means a multi-site group with its own finance lead. Most single practices stay in the first group for longer than their owners expect.
When Outsourcing Fits
A single clinic with a practice manager, a handful of contractor doctors and one set of bank accounts rarely produces a full-time bookkeeping load. That is the case to outsource healthcare accounting services before you hire, and to revisit it when you add a site.
When an In-House Hire Fits
Once a group runs several sites and dozens of practitioners, someone on site earns their salary. The usual model at that size is a finance lead in house, with outsourced support underneath for the close, payroll and the wider accounting for medical practice groups. Our outsourced accounting services cover that layer above the bookkeeping.
Patient Privacy With an Offshore Team
Regardless of turnover, the Privacy Act covers any business that is a health service provider, so the small business exemption never applies to your clinic. If personal information goes to a team overseas, Australian Privacy Principle 8 requires reasonable steps to make sure that team handles it in line with the principles, and your practice stays accountable for any breach. Our team works from India. The books need billing totals, never clinical notes, so scope access that way.
Do Medical Practices in Australia Charge GST on Medical Services?
Generally, no. The ATO treats a medical service as GST-free when a Medicare benefit is payable for it, or when it is supplied by or on behalf of a medical practitioner and is generally accepted in the medical profession as necessary for the patient’s appropriate treatment. The exceptions are where practices get their BAS wrong, because they flow through the same system and bank account.
Services Billed on Behalf of a Doctor
A nurse’s service can share the doctor’s GST-free status when it is billed in the doctor’s name, the doctor accepts full responsibility, it forms part of the doctor’s service and the doctor is involved in at least part of it. A referral is different. The physiotherapist or specialist you refer to is assessed on their own service.
Where GST Does Apply
Cosmetic procedures with no Medicare benefit payable, such as tattoo removal, are taxable. So is a report written for an insurer or a law firm where no Medicare benefit is payable and the report is not a natural part of treating the patient. Workers compensation progress reports and injury litigation reports are the common examples, and both are supplied to a business, not the patient.
Coding Mixed Supplies for the BAS
A practice that bills both kinds needs separate income accounts for GST-free and taxable supplies, and its GST credits on costs follow the same split. Getting GST on medical services right at the point of entry means the BAS reconciles to the ledger, instead of being rebuilt from memory every quarter.
Does Payroll Tax Apply to Medical Centres That Use Service Fee Arrangements With Contractor Doctors in Australia?
It can. Payroll tax is a state tax, and the contractor provisions in each state’s legislation can treat payments to doctors as wages even when the doctor is not an employee and the agreement is called a service fee or room rental arrangement. The answer turns on the facts of each agreement and the state you operate in, which is why the ledger has to hold the facts.
The Relevant Contract Rules
Revenue NSW states that payments to practitioners who are not employees may still be subject to payroll tax under its relevant contract provisions, and cites two appeal decisions, Thomas and Naaz Pty Ltd in New South Wales in 2023 and The Optical Superstore in Victoria in 2019. The Act holds seven contractor exemptions, so an exemption has to be tested, not assumed.
The NSW Bulk Billing Support Initiative
Since 4 September 2024, a New South Wales medical centre can claim a payroll tax rebate on GP contractor payments if at least 80 per cent of its GP services are bulk billed or billed under veterans’ arrangements in metropolitan Sydney, or 70 per cent elsewhere. The test counts every GP service at the centre, including those by employed GPs, and the rebate has no end date. It does not extend to employed GPs, non-GP specialists or allied health.
What the Books Have to Show
The ledger needs gross billings per practitioner, the service fee retained and the amount paid out, plus the bulk billing proportion per site if you claim the rebate. We keep those figures by practitioner every month, and our payroll outsourcing team runs the pay side.
What Is the Best Accounting Software for a Medical Practice in Australia?
For most Australian practices the best accounting software for medical practice work is Xero, with MYOB the alternative when payroll is complex or your accountant already runs it. The bigger decision is how the accounting file connects to your medical practice management system, because that connection is where reconciliation either works or breaks every month.
Xero
The default in Australian general practice. Bank feeds, GST and BAS reporting, payroll with Single Touch Payroll, and the widest set of connections to healthcare practice systems. Its tracking categories let us report billings and fees by practitioner and by site without a separate file for every doctor.
MYOB
Strong Australian payroll and award handling, and still the system many established practices and their accountants use. If your practice runs on MYOB and it works, we work in it. Changing accounting software is a project worth doing for a reason, never out of habit or because a provider prefers it.
QuickBooks Online
Workable for a solo practitioner or a small clinic with simple payroll. It covers bank reconciliation, invoicing and reporting well. Larger practices tend to outgrow it on award payroll and on reporting by practitioner, which is usually the point at which a move to Xero is worth costing.
Practice Management Systems
Best Practice, MedicalDirector, Zedmed, Cliniko and Halaxy handle appointments, clinical records and patient billing. None of them replaces the ledger. Their billing reports are the source document we reconcile every deposit against, so the right setup is the practice system feeding totals to the accounting file, never patient detail.
Cash Flow and the Numbers a Practice Should Watch
A practice can be profitable and still short of cash, because its income arrives on four timetables while wages, super and rent leave on fixed dates. Reconciled books are the input. These five measures are what owners and practice managers should read from them every month, alongside the profit and loss.
Cash Flow Timing
Bulk billed claims, HICAPS settlements, private invoices and the quarterly incentive payment all land on different days, while payroll, super within 7 business days of payday and the quarterly BAS go out on fixed ones. A rolling 13-week cash forecast built from the reconciled ledger shows the tight weeks before they arrive.
Revenue per Practitioner
Gross billings per doctor per session, split by bulk billed, private and third-party work. For contractor doctors, the practice revenue is the service fee retained, not the gross billings, so measure the fees each room earns against what that room costs to run.
Overhead Ratio
Operating costs excluding payments to practitioners, divided by the revenue the practice keeps. Tracked monthly, it shows whether a new nurse, a longer opening day or a rent review is paid for by the extra billings. The useful comparison is your own trend, month on month.
Debtor Days
Outstanding receivables divided by billed revenue, multiplied by the days in the period. Bulk billed work barely registers, so the number is driven by insurers, workers compensation, third-party reports and rejected claims that were never resubmitted. Rising debtor days usually mean nobody owns the chasing.
Equipment and the Instant Asset Write-Off
Practices with aggregated turnover under AUD 10 million that use the simplified depreciation rules can immediately deduct the business portion of each asset costing less than AUD 20,000, where it is first used or installed on or after 1 July 2023. The books need a fixed asset register with purchase and first-use dates, so your registered agent can claim it.
Practice Structures and the Books Each One Needs
Which structure suits a practice is a decision for your registered agent and adviser. What the bookkeeping has to do differs by structure, and getting that wrong is how private spending ends up in the practice ledger and practice costs end up in a doctor’s personal return.
Sole Trader Doctors
One person, one ABN, often a contractor doctor paying a service fee to a medical centre. The books need the gross billings, the fee deducted and the net received recorded separately, plus a clear split between business and personal spending on the same card.
Partnerships
Two or more principals sharing profit by agreement. The ledger needs a capital and drawings account for each partner, reconciled monthly, so the year-end profit split matches the partnership agreement rather than whatever each partner happened to draw.
Companies
A Pty Ltd practice has its own bank account, its own file and stricter records: the ATO requires most records for 5 years, and ASIC requires companies to keep theirs for 7. Money a director takes out that is not a wage or a dividend becomes a loan account to track all year.
Trusts and Service Entities
Many practices run a service entity that employs the staff and charges the practitioners or the practice a fee. Each entity needs its own file, the fee invoiced every month, and the intercompany balances reconciled on both sides, or the arrangement falls apart at year end.
What Are the Best Bookkeeping Services for Doctors and Medical Practices in Australia?
The best bookkeeping services for doctors in Australia reconcile Medicare and HICAPS settlements to your billing report, report by practitioner, publish a price, and are clear about who lodges. Judge every provider, including us, on those four tests before you look at the logo list or the review count.
Settlement Reconciliation
Ask any provider of bookkeeping for medical practices how they reconcile a bulk Medicare deposit back to individual doctors. A provider that matches deposits to income without the billing report is recording what arrived, not what was earned, and the fees, gaps and rejected claims quietly disappear from the numbers.
Reporting by Practitioner
A practice-wide profit and loss hides the question owners actually ask: which doctors, sessions and billing mixes cover their share of the costs. Medical practice accounting that cannot answer that question each month is general bookkeeping with a medical label on the proposal.
A Price You Can See
Specialist firms publish fees from AUD 250 to AUD 2,100 a month. A firm that only quotes after a call is not necessarily dearer, but get the scope in writing, with bookkeeping, payroll, practitioner statements and BAS preparation priced as separate lines so two quotes can actually be compared.
Who Lodges
Under the Tax Agent Services Act 2009, only an agent registered with the Tax Practitioners Board may provide BAS or tax agent services for a fee. We prepare, your registered agent lodges. Specialist medical accountants and accountants for doctors who hold that registration both lodge and advise, and their accounting services for doctors are the right call when structure and tax planning matter more than the monthly books.
Practices We Keep Books For
Healthcare accounting is not one industry. Each type of practice breaks in a different place, so healthcare accounting services have to start from that break rather than from a standard chart of accounts.
GP Clinics and Medical Centres
Mixed billing, contractor doctors, the bulk billing incentive and often a payroll tax question, all in one ledger. The weekly work is settlement reconciliation and practitioner statements.
Specialist Rooms
Higher fees, fewer patients, more private billing and gap payments, and often a company or trust behind the rooms. Debtor days matter more than volume, because one slow insurer can hold a month of revenue.
Dental Practices
Mostly private patients, HICAPS rebates, lab fees and associate dentists on percentage arrangements. Those raise the same payroll tax question as contractor GPs, and the New South Wales GP rebate does not cover them.
Allied Health Clinics
Physiotherapy, psychology and other clinics with practitioners on percentage splits, Medicare items under care plans, and NDIS-funded clients whose payment requests run through a separate portal and timetable.
How the Handover Works
Moving your practice books should not mean moving your data. The file stays in your own subscription, and the change is who has access to it.
Access to Your Own File
If your books already sit in your own Xero, MYOB or QuickBooks subscription, switching is a change of user access, not a migration. Every historical transaction stays where it is, and you can remove our access at any time.
Clean Up Before Reporting
Behind by a quarter or by three years, the ledger is brought up to date before any reporting starts. There is no point producing practitioner reports from a file nobody trusts, so the catch-up comes first.
Mapping Every Payment Stream
Each income stream and each practitioner arrangement gets its own place in the chart of accounts: Medicare, DVA, HICAPS, card terminal, private invoices, service fees retained and amounts paid out. That mapping is what makes every later reconciliation a check.
The Monthly Rhythm
Settlements reconciled as they land, practitioner statements each pay cycle, and the month closed and reported by the date we agree with you. BAS workpapers go to your registered agent each quarter with time to review.
Why Practices Move Their Books to Us
One Team on Your File
The same people reconcile your deposits each month, so nobody relearns which doctor is on which split or which fund settles late.
Australian Business Hours
Our working day is set against Australian hours, so a query your practice manager raises in the morning is answered the same day.
A Fixed Fee Agreed First
Scope sets the fee before the month starts. A heavy flu season or a new doctor joining mid-quarter does not arrive as a larger invoice.
A File Your Agent Can Sign
Reconciled control accounts, practitioner statements and BAS workpapers, delivered with time to review, so your registered agent works on the tax position instead of repairing the ledger.
Your reconciliation and reports are with you by an agreed date each month, and if we are going to miss it you hear it from us first. Your BAS workpapers reach your registered agent with time to review them, never on the due date. Your data stays in your own Xero, MYOB or QuickBooks subscription, so if you ever leave you take everything with you.
Medical Bookkeeping Questions From Australian Practices
How much does a bookkeeper charge per hour in Australia?
Employed bookkeepers earn a median AUD 1,400 a week full time, about AUD 36.84 an hour across a 38-hour week, before super. An outsourced hourly rate is not comparable to that figure, because it also covers review, software and leave cover. For a practice, a fixed monthly fee is easier to compare, since reconciliation hours swing with billing volume.
What does healthcare accounting do?
It records, reconciles and reports the money a health practice earns and spends under the rules specific to health: GST-free medical services, Medicare and health fund settlements, payments to practitioners who may or may not be employees, and payroll tax on those payments. Accounting for medical practices adds the year-end file and structure questions on top, which is where medical accounting firms usually start.
Does our bookkeeper need access to patient records?
No. Bookkeeping needs deposit reports, billing totals by practitioner, supplier invoices and payroll data. Clinical notes and patient histories are never required, so set up the access as financial reports only from the start. That one decision is the simplest privacy control a practice working with any outside provider has.
When should a medical practice register for GST?
When its GST turnover reaches AUD 75,000, measured over the current month and previous 11, or projected over the current month and next 11. GST-free sales are not on the ATO’s list of exclusions from GST turnover, so GST-free consultations count toward the threshold. Registration is due within 21 days, and registering does not mean charging GST on GST-free services.
What is assignment of benefit, and how does it affect the books?
When you bulk bill, the patient assigns their Medicare benefit to the practitioner as full payment. From 1 July 2026 the agreement can be made before or after the service, on paper or electronically, and must be kept for 2 years from the claim. In the books, a bulk billed service has no patient debtor, so any unpaid claim is a rejection to resubmit, not a patient to chase.
How long does a medical practice need to keep financial records?
Most tax and super records for 5 years, starting from when the record was made or the transaction completed. Companies keep records for 7 years under ASIC rules, assignment of benefit agreements are kept for 2 years from the claim, and some records must be kept longer than 5 years where they cover an assessment still open to review.
Start Medical Bookkeeping in Australia With GATP
Send us your last BAS, one month of Medicare and HICAPS settlements, and how you pay your doctors. We will show you what the reconciliation looks like, what it costs on a fixed fee, and what we would fix first.