Practice Updates - October 2025

Upcoming R&D Tax Incentive application deadline and DISR processing times 

Companies with an income year ending 31 December 2024 must lodge their R&D Tax Incentive registration with the Department of Industry, Science and Resources (DISR) by 11:59 pm (AEST), Friday 31 October 2025, through the R&D customer portal. 

Those unable to meet the deadline can request an extension via the same portal, ideally before the due date. Extensions are not automatic and are assessed based on the reason provided, supporting evidence, and prior extension history. 

Companies should factor these timelines into tax lodgment and cash-flow planning, especially if expecting R&D refunds. 

Australia–UAE Comprehensive Economic Partnership Agreement - What it means for you 

Effective from 1 October 2025, the Australia–United Arab Emirates Comprehensive Economic Partnership Agreement (CEPA) opens significant new trade and investment opportunities. The UAE, Australia’s largest Middle Eastern partner, now serves as a gateway to the broader Gulf region under this landmark deal. 

Key Highlights 

• Over 99% of Australian exports to the UAE will enjoy tariff elimination - many immediately, others phased over 3–5 years. 

• Expected tariff savings: up to AU$135m in the first year, reaching AU$160m by year five. 

• Covers 120+ service sectors (including legal, finance, education, and health) with up to 100% foreign ownership allowed. 

• Simplified customs rules, preferential duty rates, and easier skilled labor mobility (for visitors, transfers, and service suppliers). 

What Businesses Should Do 

• Map your products to CEPA tariff schedules to identify immediate and future savings. 

• Review compliance processes - ensure correct rules of origin and certificate documentation. 

• Optimise UAE operations: consider distribution partners or wholly owned setups where permitted. 

• Digitise trade records and explore automation tools to speed up customs clearance. 

• Align offerings with UAE priorities in renewable energy, manufacturing, and digital commerce. 

Employees incorrectly treated as independent contractors 

Businesses that incorrectly treat employees as independent contractors face serious ATO and Fair Work penalties. These can include: 

• PAYG withholding penalties for not deducting and remitting tax from employee payments. 

• Super Guarantee Charge (SGC) liabilities, which exceed normal super contributions and include interest, admin fees, and penalties of up to 200% of the SGC. 

• Fair Work Act penalties for sham contracting, where an employee is misrepresented as a contractor - courts can impose significant fines on businesses or individuals involved. 

Businesses should regularly review worker arrangements to ensure compliance and report suspected sham contracting to the Fair Work Ombudsman. 

Separating fact from fiction on accessing your super early 

Accessing superannuation early is tightly regulated and only allowed in limited cases. The two main grounds are: 

• Severe financial hardship - if you receive qualifying Centrelink or DVA payments and cannot meet essential living costs. 

• Compassionate grounds - to prevent home foreclosure, or to pay for life-threatening or chronic medical treatment. 

Applications must be made to the ATO via MyGov, with full supporting evidence. The ATO has warned against third parties and medical providers exploiting this system for cosmetic procedures, which are not valid grounds. Accessing super illegally or providing false information can result in severe penalties for both individuals and SMSF trustees. 

Final month to lodge: NFP self-review returns due 31 October 2025 

Non-charitable not-for-profits (NFPs) with an active Australian business number (ABN) that self-assess as income tax exempt are required to lodge an annual NFP self-review return by 31 October each year, unless they have an ATO-approved substituted accounting period (SAP). 

If your NFP has a standard tax year of 1 July to 30 June, the NFP self-review return must be lodged by this month. Penalties may apply for late lodgment. 

You don't need to lodge an NFP self-review return for income years prior to 2023–24. 

South Australia payroll tax - Ruling for medical practitioners 

RevenueSA has updated its payroll tax ruling (PTASA004v3) to provide further clarification on the retrospective payroll tax amnesty and the bulk-billing exemption for general practitioners (GPs) and other medical professionals. 

The amnesty applies to unpaid payroll tax on wages paid to GPs and certain specialists up to 30 June 2024. 

From 1 July 2024, an exemption will apply to wages paid to GPs for bulk-billed services, with the exemption’s availability being based on the practice’s bulk-billing rate. 

The latest update clarifies how bulk billing is treated when GPs work across multiple practices and builds on earlier changes relating to bulk-billing incentive payments. 

Arbitration process Formalised under Australia-New Zealand MLI 

The ATO and the New Zealand Inland Revenue have released their Memorandum of Arrangement concerning the mode of application of the arbitration process that is provided for under Part VI of the Australia-New Zealand double tax treaty, as modified by the Multilateral Convention to Implement Tax Treaty Related Measures to Prevent Base Erosion and Profit Shifting (the MLI). The Memorandum of Arrangement is effective on 2 September 2025. 

We will keep you updated as further practical guidance or developments become available. 

Speak with Lynden Group today to safeguard your business, minimise penalties, and stay ahead of ATO recovery action. 

Office: 03 91157406   

Direct: 03 85481843  

Email: info@lyndengroup.com