Auditors from his office in the eThekwini municipality received death threats, leading to the provincial leader in KwaZulu-Natal withdrawing their services from the metro.
The KwaZulu-Natal department of Co-operative Governance and Traditional Affairs said it would investigate.
Makwetu said Parliament and the National Assembly committee on the auditor-general must intervene.
He said the threats occurred in departments, municipalities and state-owned entities.
He said he believed the push-back against him would continue in state institutions after the Public Audit Bill, which gives him more powers to act against graft, has been signed into law.
He said officials would fight back as the new law would allow him to refer cases to the Hawks, the police and the Public Protector for investigation.
The latest municipal audit report released last week, found irregular expenditure had significantly increased, from R16.2 billion to R28.3bn.