Where this occurs, it can make things very difficult for the client, Ms Schaefer said.

“All of a sudden they won’t be able to get SuperStream contributions through or clearing house contributions through or rollovers done, particularly where they’re rolling in or out of an APRA-regulated fund,” she said.

Once the lodgements are brought back up to date, it will still take a minimum of 21 days for the fund’s registration details to be put back up, she said, which can be problematic for funds that already have transactions pending.

“They’ve certainly been a lot more active around this than they have been in the past, and I suspect that will continue,” she said.

The ATO has been closely monitoring the late lodgement of SMSF returns for a number of years, warning SMSFs back in 2014 that it would be taking action against funds with two or more years’ worth of overdue returns.

Since the launch of its non-lodgement program last year, the ATO has seen a reduction in the number of non-lodgers across the SMSF population, with the number of overdue lodgers falling from 87,000 down to 66,000 in February this year.

The ATO has had a strong focus on SMSF professionals that have fallen behind on their obligations in particular, with the Tax Office taking action against hundreds or tax agents and SMSF auditors outstanding SMSF returns.

Last month, ATO assistant commissioner Dana Fleming said following the ATO’s activity in this area, over 1,000 late returns were lodged by tax agents.