Johannesburg - Only 5% of municipalities obtained clean audit reports in the financial year 2011/2012, the auditor general disclosed on Monday.
However, auditor general Terence Nombembe said he was excited by the fact 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.
But 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 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.