Under its new penalty powers, the ATO has also handed out approximately 54 education directions and 27 rectification directions, Ms Simmons said.

The powers, introduced in July last year, allow the ATO to impose administrative penalties on trustees for certain SIS Act breaches.   In addition, the powers allow the ATO to direct SMSF trustees to fix a breach and direct trustees to undergo education in the event of a breach.

"We haven't seen the penalties themselves cause a significant shift in what contraventions are being reported or the number of contraventions themselves that are being reported," Ms Simmons told delegates at the SMSF Association's state technical conference in Sydney this week.

"That could also be just a function of timing. When you think that penalties apply to contraventions from 1 July 2014, and the reporting timelines, and when most SMSFs would lodge – we are still waiting on a lot of that intel to come through."

Discussing administration penalties, Ms Simmons noted that from 31 July this year, there will be an increase in the penalty units from $170 to $180.   This new figure will apply to all contraventions that take place after 31 July this year. The figure will also be indexed every three years from 1 July this year.

In light of recent confusion, Ms Simmons also stressed that the lodgement of an auditor contravention report does not automatically result in a penalty for a trustee or member.