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How does payroll tax work in the Northern Territory?

Payroll tax in the Northern Territory (NT) works similarly to other states in that it's a self-assessed tax. This means if you employ staff in Australia, it's your responsibility to figure out whether you're liable for payroll tax. It's also your responsibility to calculate how much tax you need to pay and lodge your returns by the deadline.

This guide covers the specifics of payroll tax in the NT, including thresholds, rates, exemptions and how to register. 

Payroll tax threshold and rate in the Northern Territory

The payroll tax threshold and rate in the Northern Territory differ from those in the other states and territories. 

In the Northern Territory, the payroll tax threshold is $125,000 per month, or $1.5 million a year. If your total taxable wage bill is lower than this, you don't have to pay payroll tax.

The payroll tax rate in the Northern Territory for annual total wages over $1.5 million is 5.5%. 

How do you calculate payroll tax in the NT? 

To calculate payroll tax in the NT, you apply the rate of 5.5% to your taxable wages in excess of $125,000 a month or $1.5 million a year.

When you lodge your total wages with the Territory Revenue Office’s online payroll tax portal INTRA, the system calculates your monthly and annual liability based on the information you supply. 

When is NT payroll tax due and payable? 

NT payroll tax is due and payable by the 21st of each month. If you pay over $125,000 in wages in a month, you immediately become liable for NT payroll tax. Once liable, you must register and pay by the 21st of the following month. For example, if you pay employees $125k in wages in January, you'll need to register for payroll tax, lodge a return and pay the calculated tax value by 21 February. 

Annual reconciliation for Northern Territory businesses

The annual reconciliation for Northern Territory businesses is also known as an annual adjustment return (AAR) and must be lodged through the integrated revenue application (INTRA) by 21 July.

The AAR makes sure you've paid the correct amount of payroll tax for the year according to your total wage bill. If you haven't paid enough payroll tax, you'll need to pay the difference. If you've paid too much, you can apply for a refund from the Territory Revenue Office (TRO)

Payroll tax exemptions available in the NT

Payroll tax exemptions available in the NT apply to certain types of wages, employees and employers. Wages exempt from payroll tax include:

  • Parental/adoption leave

  • Payments to staff on military reserve leave

  • Redundancy payments (under the tax-free threshold)

  • Payments to employees who have worked for you overseas for over six months

If you're a non-profit employer, you might be able to apply for payroll tax exemption. Non-profit employers include charities, religious institutions, some schools or colleges, local governing bodies and most hospitals.

Northern Territory residents may also be exempt. That is, the wages you pay people who live in the NT may not need to be included in your payroll totals. 

Northern Territory employer groupings for payroll tax 

Northern Territory employer groupings for payroll tax occur when two or more businesses are controlled by the same person, people or business entity.

If you're part of an employer grouping, make sure that everyone is aware of their payroll tax obligations and that you're using the best payroll systems to stay compliant. Only one member of your group can claim a tax-free threshold, so the rest of the group needs to pay payroll taxes on the full value of their NT wages.

As an employer grouping, you're all jointly liable for payroll tax payments. This means that if a group member fails to pay on time, the payroll tax can be taken from your business instead. 

What is the integrated revenue application (INTRA)? 

The integrated revenue application (INTRA) is the online system used to manage payroll tax obligations in the Northern Territory. INTRA makes it easy to lodge your monthly and annual returns, calculate your payroll tax owed and pay your bill online. 

How do you register for payroll tax in the NT? 

To register for payroll tax in the NT, you'll need to sign up through INTRA. If you're new to INTRA, you can fill out a new user registration form. You'll need your Australian Business Number (ABN) handy to complete your registration. 

Payroll tax penalties 

Payroll tax penalties may be issued if you don't register or lodge your monthly returns or AAR by the deadline. Here, we explain some terms related to non-payment, underpayment and late payment penalties. 

Default assessment 

A default assessment, or tax default, is the TRO's estimate of how much payroll tax you owe. It's issued if you pay your tax late, don't pay the right amount or don't pay at all. Without accurate details of your wage bills, the default assessment can be much more expensive than registering and lodging your returns properly and on time. 

Penalty tax 

Penalty tax is a one-off calculation based on the amount of payroll tax you've underpaid. The penalty tax rate will depend on your circumstances, ranging from 2% to 95%. You may also be charged interest, so if you miss a payroll tax payment or make a mistake when lodging your return, you should inform the TRO right away. 

Northern Territory payroll tax FAQs

Is superannuation subject to payroll tax in the Northern Territory? 

Yes, superannuation is subject to payroll tax in the Northern Territory. Like most other employee benefits, superannuation falls under the definition of wages for payroll tax purposes. 

What is a payroll tax exemption? 

Some organisations, such as charities, religious institutions, not for profits and public hospitals, may be exempt from payroll tax. NT employers liable for payroll tax may not need to pay it on the following wages: redundancy, maternity, paternity and adoption leave, paid parental leave, defence force, volunteer emergency workers and workers compensation. Find out more about payroll tax for employers in NT. 

Master payroll tax management with MYOB

With terms like penalties, compliance and audits floating around, managing your payroll tax sounds intimidating. But it doesn't have to be. Our cloud payroll software streamlines and automates your payroll while tracking your wage bill. This helps you stay compliant while keeping payroll running smoothly, helping you improve employee management and boost workplace productivity.  

Get started with MYOB payroll software today. 


Disclaimer: Information provided in this article is of a general nature and does not consider your personal situation. It does not constitute legal, financial, or other professional advice and should not be relied upon as a statement of law, policy or advice. You should consider whether this information is appropriate to your needs and, if necessary, seek independent advice. This information is only accurate at the time of publication. Although every effort has been made to verify the accuracy of the information contained on this webpage, MYOB disclaims, to the extent permitted by law, all liability for the information contained on this webpage or any loss or damage suffered by any person directly or indirectly through relying on this information.

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