Secretary to Parliament Gengezi Mgidlana has been "granted" special leave by Speaker Baleka Mbete and the National Council of Provinces chairperson Thandi Modise following a raft of corruption allegations.

"The Secretary to Parliament wrote to the Presiding Officers on May 29, requesting to be placed on special leave while allegations levelled against him by the National Education, Health and Allied Workers’ Union (Nehawu) are investigated," Mbete said in a statement on Friday.

His leave is effective from Friday.

Mbete reiterated that they have referred several allegations regarding administrative irregularities against Mgidlana to an "independent audit committee" of Parliament for investigation.

"The independent audit committee, comprised of external individuals in line with provisions of the Financial Management of Parliament and Provincial Legislatures Act, is expected to probe the allegations with the necessary swiftness and to report back to the Presiding Officers."

Mbete stressed that "consistent with the principles of natural justice, the Secretary to Parliament remains innocent until proven otherwise."

One of the two deputy secretaries to Parliament will be appointed to act while he is on leave.

Nehawu's Parliament branch on Tuesday called for Mgidlana's immediate suspension, and threatened to bar him from entering his office if he was not suspended by the end of the week.

They said they would not be happy with special leave, which effectively meant he would sit at home and earn a salary.

"We are saying no to special leave. Mgidlana should be suspended, no special preferential treatment. We are sick and tired," said branch chairperson Sthembiso Tembe.

"If they fail to do that, it should be our responsibility to go to our office and remove him, or prevent him from entering the office," he said to vigorous applause from members.

Mgidlana is accused of irregularly, among other things, hiring senior management staff amid a budget crunch, awarding himself an education bursary at the expense of junior staff, and embarking on "wasteful and unauthorised" overseas trips.

The call also comes in the middle of a wage negotiation between Parliament and the union, after it was announced Parliament workers would receive a 0% salary increase this financial year.

Tembe accused Mgidlana of negotiating in bad faith.

Failure to suspend Mgidlana would lead them to the view that he was "untouchable", a "golden boy" and accorded preferential treatment.

Mgidlana released a statement on Sunday denying the allegations against him, saying no shred of evidence had been produced to back them up.

"Central to the union's malicious allegations is a claim that the current financial difficulty is caused by financial mismanagement and/or corruption. This is a deliberately misleading, baseless and unnecessary propagation of untruths," he said.

The financial management of Parliament was regularly checked by the multiparty joint standing committee on financial management of Parliament and annually by the Auditor-General, who granted the institution a clean audit in its last report.

Nehawu's branch deputy chairperson Disang Mocumi said they will release a statement on Mgidlana's special leave later on Friday.