The public protector's office has reported a deficit of R26 million in its annual report due to rising staff and office overheads costs, and has issued another plea for a budget increase.

Outgoing CEO Themba Mthethwa notes that the chapter nine institution's budget for the past financial year was R199.2m, but spending came to R226m.

"The implication of the overspending is that the organisation will begin the financial year with a deficit of R26m."

In her foreword to the report, Public Protector Thuli Madonsela wrote: "We appeal to Parliament to relook our financial situation to ensure that our structure is fully funded while we conduct a structural review."

She warned that the office's chronic cash shortfall meant investigations took too long to complete and this could result in a loss of public trust.

"Needless to say, the acute funding and human resource constraints result in cases taking too long to complete and this has the potential to erode public trust in the institution," she said.

"In addition, the cases are becoming a lot more complex and this puts stress on the balance between swiftness and thoroughness."

In July, Madonsela told Parliament's portfolio committee on justice that her budget was being strained by rising litigation costs as ministers increasingly challenged her findings.

In the report she notes: "On remedial action, we appeal to Parliament and provincial legislatures to join hands with us in ensuring remedial action, as envisaged in section 182 of the Constitution, is not replaced by impunity."

This week, a parliamentary ad hoc committee consisting of only ANC members after the opposition withdrew from it, rejected her directive to President Jacob Zuma to repay part of the R246m in state funds spent on his private homestead in Nkandla, KwaZulu-Natal.