"In some cases, auditors are given instructions that 'you will sweep this under the carpet,'" Claudelle von Eck, the association's CEO, was quoted as saying in the Sunday Independent.

"It becomes worrying because internal auditors are meant to be the whistle-blowers."

She said some members had reported intimidation, but the association had no power to intervene.

Auditor General Terence Nombembe revealed on Monday that only 5% of municipalities obtained clean audit reports in the 2011/2012 financial year.

Nombembe said he was excited that six new municipalities had joined the clean audit category, taking the number to 13.

The municipalities with clean audits were in KwaZulu-Natal, Limpopo, Mpumalanga, and the Western Cape.

None of the municipalities in the Eastern Cape, Free State, Gauteng, Northern Cape and North West received clean audit reports.

Nombembe said almost half (45%) obtained unqualified audit reports, but with concerns.

These municipalities received unqualified reports after corrections during the audit process.

Among the issues identified as a challenge were procurement, service delivery, and errors in financial information.

None of the country's metros received clean audits while 13% of municipalities did not submit financial statements in time for auditing.

There are currently 343 municipalities in the country.

Nomembe commended municipalities which were putting in an effort to obtain clean audit statements.

"They are moving forward towards the clean audit space by consistently committing to take ownership of municipal performance practices, insisting on adequately qualified staff and effective performance management practices," said Nombembe.