Self-managed superannuation fund (SMSF) audit requirements are still being ignored by many tax agents, according to the Australian Taxation Office (ATO).

The ATO said it was concerned some tax agents were signing themselves off as the auditor of the SMSF annual return, when they were not legally qualified to conduct the audit or had not actually conducted the audit.

The ATO's finding presented a situation of unease, National Institute of Accountants deputy chief executive Andrew Conway said.

"Any breach of the auditing requirements is a concern. In any situation there will be outliers who ignore the requirements, but it is incredibly important that the audit is done correctly. The whole issue of auditing quality and independence is at play here," he said.

All SMSFs need to be audited by an approved auditor before the lodgement of the annual return. Approved auditors can be a registered company auditor or a member of a professional association, for example CPA Australia, the Institute of Chartered Accountants in Australia and the National Institute of Accountants.

While trustees needed to understand the importance of the audit process, it was also the responsibility of advisers to ensure trustees understood their requirements under the regulations, Conway said.

There was also the further issue where accountants had to understand where the line was in terms of where independence became impaired, he said.