Bosses who deliberately underpay or withhold compulsory superannuation payments from their staff are being warned by the Australian Tax Office to end the rip-off or face steep fines.

Key points: The ATO's pursuit of dodgy employers holding back super has been boosted by the introduction of Single Touch Payroll

The ATO's pursuit of dodgy employers holding back super has been boosted by the introduction of Single Touch Payroll The system has so far allowed nearly 500,000 employers to report every payday for 11 million employees rather than annually

The system has so far allowed nearly 500,000 employers to report every payday for 11 million employees rather than annually And the ATO has recently scrutinised 75 million transactions for 400,000 businesses using the cross-matching system

Reminder emails — described by the ATO as a "nudge" — will go to 4,000 employers with a track record of late super payments and another 500 bosses who have failed to pay the right amount by the quarterly date.

The crackdown will target known offenders in the super rip-off, including cafes, restaurants, clubs, supermarkets and tradie subcontractors in the construction industry, but also architectural, legal and advertising firms.

Deputy Tax Commissioner James O'Halloran told the ABC's AM program that employers who failed to lodge superannuation guarantee payments were robbing their staff and would be asked to explain the non-payment.

"It does seem to be in a range of service-type industries. Sometimes it's obviously some cashflow pressures. But ultimately, by not paying the superannuation guarantee, the employee misses out on money for their retirement future," Mr O'Halloran said.

James O'Halloran said about 4 or 5 per cent of businesses appeared not to be paying. ( Supplied )

"We still encourage people to come forward to the ATO, should they believe that they have not been paid their super guarantee. But of course, we can match patterns now and look for people who continually pay late or don't pay the correct amount."

The ATO's pursuit of dodgy employers who hold back compulsory super has been boosted by the introduction of Single Touch Payroll where nearly 500,000 employers now report every payday for 11 million employees rather than annually.

Under the mandatory superannuation guarantee, employers are required to contribute the current minimum 9.5 per cent into the super funds of any worker aged 18 and over, earning $450 a month.

Sorry, this audio has expired The Tax Office is targetting bosses who hold back super guarantee

Mr O'Halloran said the ATO recently scrutinised 75 million transactions for 400,000 businesses using cross-matching systems including Single Touch Payroll.

"There will be 500 businesses that we will be following up who do not appear to be paying what they are committed to pay.

"So their employee does not appear to have got the payment that they should have got, that was promised to them," Mr O'Halloran said.

"We think there's about 4 or 5 per cent of businesses that appear not to be paying.

"Depending on the response we get from people, there will be some follow-up, as well as the possibility of some reviews and audits and, therefore, some penalties."

The ATO estimated in 2017 that rogue employers short-changed staff by an average $2.81 billion every year between 2009 and 2015.

Industry Super Australia has claimed that around a third of Australian workers have been ripped off by bosses who withhold all or some of the superannuation guarantee.

Mr O'Halloran said the ATO was at the beginning of a "very proactive and very intentional follow-up" with employers.

"Come forward now, or the penalties and the sanctions will be more serious. Do the right thing: pay your employees what they are entitled to," Mr O'Halloran warned.

The ATO has recovered $805 million in unpaid super from 23,000 businesses over the past year.