Is Your Medical Practice Ready for the New Payroll Rules?

Health professional practices are entering a new era of payroll compliance. With Payday Super now in effect, health professionals need to ensure employee wages, superannuation and payroll systems are accurate, compliant and up to date.

Importantly, there is no concession for wages paid to yourself or related parties. This, combined with the need to flow money to the practitioner under the Personal Services Income (PSI) rules, means more care needs to be taken when setting your own wage and superannuation levels. In a perfect world, the goal is to pay out all of the taxable profit by year end, with a small adjustment completed during tax planning in June each year. Failure to get the levels right could result in amended BASs, denied deductions for superannuation payments, penalties and interest.

What Has Changed?

From 1 July 2026, employers are required to pay employees’ superannuation at the same time as salary and wages, replacing the previous quarterly payment system. Super contributions generally need to reach the employee’s nominated super fund within seven business days of payday. At the same time, STP continues to provide the Australian Taxation Office (ATO) with real-time payroll reporting, making payroll accuracy more important than ever. This makes backdated adjustments almost impossible and means there is a greater risk of denied superannuation claims.

Unfortunately, the interaction of the new Payday Super rules with the existing Personal Services Income legislation has created a potential issue for health professionals, particularly where they operate through corporate structures. There is now a real need to set appropriate wage levels early and consider superannuation contribution limits in advance.

The additional reporting also means the ATO has the ability to audit and detect more issues in a more timely manner. As a result, Holmans expects to see a significant increase in compliance letters and employee superannuation audits, including superannuation relating to your own wages.

Other Matters to Review

As outlined in prior articles, now is the time to check your current employee details, including the award they are employed under, their superannuation fund details, HECS withholding, PAYG withholding settings, employee bank account details, and any other contract terms and conditions.

Don’t Forget Cashflow Planning

One of the biggest changes for many practices is the impact on cashflow.

Previously, businesses could retain superannuation funds until quarterly due dates. Under the new rules, those funds leave the business each payday. While the total annual super obligation remains unchanged, the timing of payments requires practices to budget differently and maintain sufficient working capital throughout the year.

How Holmans Can Help

At Holmans, we work with healthcare professionals across the Sunshine Coast and throughout Queensland to help simplify wage setting, PAYG withholding, superannuation contribution levels and other tax compliance matters.

We recommend all health professionals review their wage levels for the current financial year and consider setting appropriate wage limits and regular superannuation payments. They should also diarise a meeting with their accountant in May or June to fine-tune final wage and superannuation payments before year end.

Need Specialist Accounting Advice for Your Health Professional Practice?

Holmans has extensive experience working with doctors, specialists, allied health professionals and medical practices across the Sunshine Coast. Learn more about our specialist services for health and medical practitioners and discover how we can help your practice remain compliant while supporting long-term growth.

Disclaimer: This article contains general information only. Regrettably, no responsibility can be accepted for errors, omissions or possible misleading statements or for any action taken as a result of any material in this guide. It is not designed to be a substitute for professional advice, as such a brief guide cannot hope to cover all circumstances and conditions applying to the law as it relates to these items.

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Phone: (07) 5430 7600 or email info@holmans.com.au