This represents around 54,000 funds out of the total 597,000 SMSFs at 30 June 2017.

“Accordingly, we implemented a strategy of differentiated treatments and initial results have seen around 12 per cent of funds taking action to wind up or bring their lodgements up to date,” the ATO said.

“We continue to actively pursue the remaining funds to either bring them back to regulatory compliance or remove them from the system.”

Last month the ATO told the SMSF Summit that around 40,000 SMSFs were now at risk of being made non-compliant and that it was undertaking audits on a significant number of funds.

The report also indicated that for 2015/16 SMSF annual returns due during the 2016/17 year, 93 per cent were on time. All SMSFs were given an extension until 1 July 2017 to enable them to better prepare for the new superannuation measures implemented from that date.

There was a slight improvement with the on time payment of tax obligations with 79 per cent of SMSF liabilities paid on time, up four percentage points from last year.

Ninety six per cent were paid within 90 days of the due date which is up two percentage points from last year.

At 30 June 2017, SMSFs owed $123.4 million in collectable tax debt, down 23 per cent from last year.