An investigation by the Australian Tax Office during the 2017-18 financial year revealed 418 ACT-based employers were found to have underpayed superannuation to their workers.

The ATO reclaimed $7.7 million in superannuation from businesses as a result of the investigation. It is not known how many ACT employees were affected by unpaid superannuation, and it is unclear how many workers have been repayed.

Employers who own a business in the ACT but are registered in another state or territory were not included in the figures.

An ATO spokesman said the obligation for superannuation payments rests with the employer, warning businesses against underpayment.

"We take non-payment of superannuation guarantee very seriously and we investigate all reports of non-compliance made to us," the spokesman said.

"While the vast majority of employers do the right thing, even a small amount of non-compliance is unacceptable."

Nationally, the ATO reclaimed $829 million in unpaid superannuation and completed almost 32,000 investigations into the practice in 2017-18.

More than 5000 Australian employers were under investigation, according to the tax office.

"In 2017-18, we received roughly 30,000 reports from people who believe that they have not had their superannuation paid by their employer," the ATO spokesman said.

"We examine every report, and where suitable, we follow up by making contact with the employer to see confirmation.

"If necessary, we conduct audits and apply penalties, which can be up to 200 per cent of the shortfall."

Under superannuation law, employers are required to pay 9.5 per cent to workers over 18 who are earning more than $450 a month.

Industry Super Australia public affairs director Matt Linden said employers underpaying superannuation contributions is endemic across Australia.

"Around one in three employees are being shortchanged in terms of super, and our analysis of tax office data is the average amount is underpaid around $2000," Mr Linden said.

"The risk of unpaid super is heightened for young people and those in occupations where work is more temporary in nature.

"It's also the case with workers where English is a second language, and there's a cohort of workers who may not be familiar with their entitlements."

Mr Linden said the current superannuation system doesn't adequately protect workers who may be getting underpaid.

Under current legislation, employers have four months to pay superannuation contributions as it appears on a worker's pay slip, and Mr Linden said this should be altered.

"A key change is to ensure that super is paid at the same time as people's wages and salaries," he said.

"Currently, the onus is on the individual to report an employer for superannuation underpayment, and that's unacceptable."

The most recent figures from the ATO on the overall superannuation guarantee gap - the difference between the theoretical amount of paid super and the amount actually paid - found employers underpaid workers by $2.85 billion in 2014-15.

That figure made up 5.2 per cent of the estimated $54 billion employers were required to pay in that time period.

Earlier this year, a Canberra law firm director was ordered to pay a $20,000 fine by the ACT Civil and Administrative Appeals Tribunal for failing to pay superannuation to employees.

The ATO spokesman said employees can use online tools to see if they are owed superannuation, or lodge an enquiry with the tax office.

"We also identify non-compliance through referrals from third parties and examination of ATO-held data, which informs reviews and audits on higher risk employers," the spokesman said.

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