How this usually works
A good tax accountant for medical will start with a short discovery: how you bill (MBS, private, insurer), who is engaged (owners, associates, contractors, employees, locums), the software stack (e.g., Xero, MedicalDirector, Best Practice, Cliniko, Genie, PracSoft), and any immediate ATO or state revenue deadlines.
Work typically falls into three layers:
- Immediate triage: correct GST/BAS coding on mixed supplies, clear STP backlogs, lodge overdue BAS/tax, address super and payroll tax exposures, and set PAYG instalments appropriately.
- Process design: refine service entity flows, practitioner contracts, remittance reconciliation, chart of accounts, car logbooks and FBT declarations, and month‑end close templates.
- Ongoing review: quarterly BAS checks, year‑end tax planning, super and payroll health checks, and proactive alerts for regulatory changes affecting medical practices.
Australian context to keep in view
- GST on medical: Services that qualify as medical services (often MBS‑billed) are generally GST‑free; cosmetic and retail sales are usually taxable. Many clinics have mixed supplies, so BAS depends on accurate item coding and evidence.
- PSI and service entities: Income splitting may be limited by Personal Services Income rules. Ensure service entity mark‑ups and agreements reflect commercial reality and current ATO guidance.
- Payroll tax risk: Several states treat certain practitioner payments as taxable for payroll tax. Contracts, rosters and control indicators matter; get state‑specific advice.
- Super and contractors: If a practitioner is paid mainly for their labour, super can be required even for contractors. The Super Guarantee rate is now 12% (confirm current rate if reading later).
- FBT hotspots: Motor vehicles, phones/data, and staff benefits need correct FBT or exemption treatment with supporting records (e.g., logbooks, declarations, minor benefits).
- Asset write‑offs: Thresholds change. Check current instant asset write‑off limits and depreciation rules before major equipment or fit‑out purchases.
- Registration: Verify your provider on the Tax Practitioners Board public register and confirm PI insurance and scope.
What to compare before you commit
Scope
Confirm the scope covers structure advice (company, trust, service entity), BAS/GST on mixed supplies, payroll tax risk review, STP & super, FBT, year‑end tax, and ATO support.
Software fit
Look for fluency in your stack (Xero/MYOB/QuickBooks + MedicalDirector, Best Practice, Cliniko, Genie, PracSoft) and clear data flow between clinical and accounting systems.
Turnaround and communication
Agree on monthly close dates, BAS review windows, response times, and an escalation path during peak periods (e.g., June/July, January).
Commercial fit
Compare fixed vs hourly pricing, what’s included, meeting cadence, and proactive planning (tax planning, equipment timing, cashflow and instalments).
Strong providers explain “why” as well as “what” — and tie recommendations to clinical operations and patient flow.
Best next steps
Write down your primary outcome: streamline BAS, clarify GST on services and products, resolve payroll tax exposure, set up a service entity, clean up STP/super, plan year‑end tax, or prepare for growth (new site or practitioners).
Pull the key documents: practitioner agreements, a recent BAS, payroll/STP summary, super remittance proof, and a P&L by income stream. This speeds diagnosis and keeps scope tight.
Then shortlist a tax accountant for medical who can demonstrate experience with similar practice models and software, provide a clear roadmap, and commit to a reporting rhythm that fits your clinic.
Use the related pages for bookkeeping and payroll support if your next move is to stabilise day‑to‑day operations before deeper tax work.
Frequently asked questions
Do medical services attract GST in Australia?
Most medically necessary services that meet the definition of a “medical service” are GST‑free, including many MBS‑billed consults. Cosmetic and other non‑therapeutic services are generally taxable. Many practices have mixed supplies (GST‑free consults plus taxable consumables or cosmetics), so correct coding and BAS review are essential.
Should I use a service entity or will PSI rules apply?
Service entities can separate clinical income from administrative services and share costs fairly. However, Personal Services Income rules may restrict income splitting if key tests are not met. Have a qualified tax accountant for medical review your contracts, control over work, and client relationships to assess PSI risk.
Are contractor doctors subject to super or payroll tax?
If a practitioner is paid mainly for their labour, super can be required even for contractors. State payroll tax may also apply to certain practitioner payments depending on contract terms and practice control. Get state‑specific advice and ensure agreements, rosters and remittances align with your intent.
What are common FBT issues in medical practices?
Cars (logbook and private use), phones/data, and staff benefits can trigger FBT. Some items may be exempt or fall under minor benefits, but you need the right records (logbooks, declarations, substantiation) and correct payroll coding.
Which deductions do doctors and clinicians commonly claim?
Professional indemnity, registration and memberships, CPD and conferences, medical equipment and tools, clinical software, work‑related portion of phones/data, and fit‑out or equipment depreciation. Instant asset write‑off thresholds change, so check current settings before large purchases.