A new auditor-general's report released on Thursday recommended the ATO better use its enforcement capabilities to get back the money entitled to workers.

It was one of three recommendations outlined in the report examining non-compliance with the superannuation guarantee.

Among the other recommendations by the audit office was to implement a compliance strategy and enhance its own performance reporting.

The tax office agreed to two of the recommendations in the report, while it partly agreed to the calls to improve performance information.

While more than 95 per cent of super payments are handed out to employees without the need for intervention by the tax office, it is estimated almost $3 billion was owed in unpaid super as of the end of the past financial year.

"The ATO's activities in addressing superannuation guarantee non-compliance are partly effective," the report said.

"Although there has been an increase in the absolute amount of debt raised and funds collected, the ATO has acknowledged that it has a small influence of the net superannuation guarantee gap."

The report noted there had been an increase in the debts raised in the past four years.

The tax office said in response to the report it would aim to beef up its powers to enforce unpaid super.

"We will make more use of our debt recovery powers now that firmer recovery action has recommenced following the pandemic," the ATO said.

"We will explore opportunities to enhance our performance measures and commentary on superannuation guarantee performance information."

The debt-recovery powers of the tax office were not fully used during 2020 during the pandemic, in line with other compliance work being suspended.

However, the report noted that super debt increased at a higher rate than total ATO debt in 2020/21.

Australian Associated Press