Payroll tax in the Northern Territory (NT) is governed by the Territory Revenue Office (TRO). It applies to employers whose total Australian wages exceed a set threshold, with a flat tax rate applied to taxable wages paid within the Territory. While NT’s system is simpler compared to some other states, employers need to understand its specific rules.
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Payroll tax is a state or territory tax charged on the wages paid to your employees. It depends on the total taxable wages you pay. Payroll tax is a responsibility of the employer, and it is self-assessed, which means that you are responsible for calculating, lodging returns and paying your own tax. Therefore, it is essential to be informed about the correct information and rulings regarding payroll tax in your area.
In 2007, efforts were made to harmonise payroll tax rulings across Australia and most rulings generally apply to all states. However, since payroll tax is administered by the state//territory government, there are differences and state-specific rulings, which should be studied and adhered to.
First, let’s go through the most recent changes to the payroll tax in NT.
When you lodge your payroll tax return in INTRA, you’ll still need to report these wages under “gross wages”, but also record them separately in the “exempt wages” section.
From 1 July 2025, employers in the Northern Territory must register for payroll tax if their total Australian taxable wages, or the combined wages of their group, are more than $208,333 in a month or $2.5 million in a year. Payroll tax will only apply to the portion of wages paid in the NT. The payroll tax rate is 5.5%.
To register, you can use the Territory Revenue Office’s online system called the Integrated Revenue Application (INTRA) - INTRA · Account · Login
You must register for payroll tax in the month after your wages first go over the monthly exemption threshold.
After the Territory Revenue Office approves your registration, you will receive an email notification. From there, you can log into INTRA to lodge your returns and keep track of your payments.
However, you may not need to register for payroll tax if your organisation is:
However, you may still need to register if your staff are involved in commercial or business activities.
Taxable wages include more than just base salaries. This broad definition ensures that all forms of employee compensation are taxed consistently and includes most payments or benefits provided to employees and contractors, such as:
You may not be required to pay payroll tax on the following payments:
In some cases, only part of these payments will be exempt.
Employers registered for payroll tax in the NT must lodge a return and pay payroll tax each month, unless the Commissioner has approved them to lodge annually. Generally, if your estimated payroll tax for the full year is less than $10,000, you will only need to lodge an annual return instead of monthly returns.
Monthly returns are lodged through INTRA, the Territory Revenue Office’s online system. Returns must be submitted and payments must be cleared by the 21st day of each month. If you have no payroll tax liability for a particular month, you must still lodge a ‘nil’ return to avoid reminder notices.
At the end of each financial year, all registered employers must lodge an Annual Adjustment Return (AAR) using INTRA. This is due by 21 July and requires you to pay any shortfall between the payroll tax already paid during the year and your full liability to 30 June, or request a refund if you have overpaid.
For payroll tax purposes, businesses can be treated as a group if they are under common control or share employees.
When businesses are grouped, only one business in the group, which is appointed as the DGE (the Designated Group Employer), can claim the tax-free threshold. This threshold is calculated based on the combined wages of all group members across Australia. Other members of the group must pay payroll tax on their full NT wages without any threshold benefit.
Groups can also apply to have their DGE lodge a single consolidated return and make one payment on behalf of all members. However, all group members remain jointly responsible for the group’s payroll tax obligations.
Payments to contractors, consultants, and suppliers may be subject to payroll tax if they meet certain conditions, such as providing services that are a regular part of your business, working more than 10 days per month, invoicing for over 90 days in a year, having no employees of their own, or if labour makes up more than half the contract value. A relevant contract is any agreement under which these services are provided (excluding simple purchases of materials or equipment). Payroll tax must be paid on payments under a relevant contract unless a specific exemption applies. Employers should assess contractor arrangements carefully to avoid unexpected payroll tax liabilities.
After lodging your annual return, you must promptly pay any difference between the tax already paid during the year and your total liability by the due date. Do not wait for the Territory Revenue Office to issue a notice of assessment.
If payroll tax is not paid on time, interest will be charged on the overdue amount and penalty tax may also apply.
If you have overpaid payroll tax, the Territory Revenue Office can apply the credit to your next financial year’s return to reduce the amount payable. If you prefer, you can request a refund instead.
Payroll tax in the Northern Territory is an important obligation for employers with total Australian wages above $2.5 million annually (or $208,333 per month). With a flat rate of 5.5%, it applies to wages paid within the Territory, including many forms of employee and contractor compensation. From 1 July 2025, significant changes, such as higher thresholds and exemptions for apprentices and trainees, make it even more important for employers to stay informed.
To stay on top of payroll tax in the Northern Territory, businesses need to register on time, lodge returns as required, and accurately report all taxable wages while applying the appropriate exemptions. It’s also important to understand how grouping rules, contractor arrangements, and interstate wages can affect your liability.
By keeping records up to date, carefully tracking payments, and using the Territory Revenue Office’s INTRA system, employers can manage payroll tax efficiently, make the most of available exemptions, and avoid mistakes or penalties. Staying proactive and informed ensures that payroll obligations are met smoothly and without unnecessary costs.
To dive deeper and know in detail about payroll tax rulings in NT, check out this guide by the TRO - Payroll tax guide