The ATO noted that a number of SMSFs have applied for deferrals, with lodgements expected to increase over the coming months.

There is currently over 138,000 lapsed lodgers with one or more outstanding SMSF returns, according to the ATO data.

The ATO warned that lapsed lodgements for an SMSF can signify “breaches of regulatory rules or illegal early release of funds”.

There has, however, been an improvement in the number of SMSF lodging their first return.

There is currently around 26,000 funds that have never lodged their first SMSF return. In late March, ATO assistant commissioner - SMSF regulatory branch, Justin Micale, reported that 34,000 SMSFs had never lodged their first return.

The ATO warned that where trustees have failed to lodge their first SMSF return, this signifies a risk that “trustees may have illegally accessed their superannuation which may to significant tax consequences and penalties”.

“It is important that SMSFs lodge their audited annual returns on time or seek a deferral from the ATO if they need additional time, to avoid unnecessary follow up,” the ATO stated.

“Lodging an annual return is a fundamental obligation of running your own super fund, and SMSFs who fail to do so are not only breaching their obligations as a trustee but are likely to trigger interest from the ATO.”

Mr Micale said in late March that lodgment of SMSF returns remains a significant priority for the ATO. 

“We have a comprehensive communication program in place to remind trustees of their lodgment requirements, including targeted mail-outs for those new to the system and those that have failed to meet a due date,” he said. 

“While this approach does deliver positive results for the majority of trustees, there remains a persistent group who continue to ignore our reminders so we’re now targeting them with a compliance campaign called three strikes and you’re out.”