“The number of outstanding SMSF annual returns for agents and auditors is at a higher level than what we would consider acceptable as we hold professionals to a higher standard when it comes to meeting their tax and regulatory obligations,” Delahunty said.

Delahunty continued that SMSF professionals could be referred to the Tax Practitioners’ Board and ASIC if there are concerns over their own or their clients’ lodgments and their registration could be put in jeopardy.

The warning from the commissioner comes off the back of data that reveals that approximately 90,000 funds still have yet to lodge their 2023 SMSF annual return (SAR).

“All key lodgement due dates for the 2023 SAR have now passed, some funds are over a year late,” he said.

“Of major concern to the ATO is that included in this population is approximately 5,000 funds who were registered in 2023 but have so far failed to lodge their first return. As new registrants, these annual returns were due for lodgement by 31 October 2023 or 28 February 2024 for SMSFs who are tax agent clients.”

Additionally, Delahunty said there are approximately 60,000 funds that have yet to lodge their 2022 SAR.

“Those who have registered and fail to lodge can expect to receive a heightened level of scrutiny from the ATO as this population is in a higher risk category for potentially illegally accessing their funds,” he said.

“Funds who are behind on lodgement will have their complying status on SuperFund LookUp (SFLU) withheld. The consequence of this is that it restricts the SMSF from receiving rollovers and employer contributions. The SFLU status won’t be reinstated until lodgement is brought up to date.”

He warned that the ATO could take further compliance action for these funds, which can result in a range of potential outcomes including trustee disqualification.