I have done an audit for ABC SMSF and found they have a lot of contraventions. I advised and provided a list of the contraventions to the accountant of the fund. The accountantant came back and wanted to put the audit on hold after it was finished so the trustees can go back to the previous accountant and get explanations of why the contraventions were not picked up in previous years. When I advised the accountant that I will be issuing the qualified audit report as I have waited long enough they advise that ABC SMSF will be going to another auditor.
I know the fund has done the wrong thing, too many breaches to be listed. In this situation what are my obligation.
Qualify for all breaches in the normal breach section (because once you hit the $30000 limit, they must all be reported, even if individually, they are not material to normally warrant it - see the ATO's 7 tests) and then in the "is there anything else you'd like to tell us" name the people involved and tell the ATO the full story, including that they left because you were doing the right thing. Because auditors lose money when we do what the ATO (and auditing standards) ask but you get trustees or accountants that lack the decency to do the right thing then blame the auditor for not allowing it.
APES110 would be even more effective if the ATO enforced against accountants and trustees who try to dodge.