South African investigators have referred 940 cases of corruption and malfeasance involving millions of dollars of Covid funds for prosecution and disciplinary action, President Cyril Ramaphosa said Tuesday.

The Special Investigating Unit (SIU), an independent law enforcement agency with similar powers to the FBI, probed 5,467 contracts awarded for Covid-19 services and supplies worth more than $900.

More than half of the contracts were found to be irregular.

"It is unacceptable that so many contracts associated with saving lives and protecting livelihoods were irregular, unlawful or fraudulent," Ramaphosa said in a statement.

With more than 3.5 million diagnosed infections and over 94,000 deaths, South Africa's pandemic toll is the highest on the continent.

The investigators have referred 386 of the cases to the National Prosecuting Authority, according to the report released to the public on Tuesday.

Another 224 cases were sent for disciplinary action against government officials, while 330 will be handed in for "administrative action", including blacklisting from public contracts.

"This investigation targeted individuals and institutions who believed they could exploit a moment of national vulnerability to enrich themselves and those with whom they colluded to abuse public resources," Ramaphosa said. 

Ramaphosa came to power in 2018 on the promise to curb corruption. He said the report marked an "important step in our fight against corruption in the public and private sectors, and against maladministration". 

He was dealt a blow when a close associate, ex-health minister Zweli Mkhize, was implicated in a Covid communications fund scandal last year.

The pandemic exposed ingrained corruption in South Africa involving politically connected and greedy government officials and business people who earned the epithet "Covidpreneurs".

In one case cited in the 737-page report, the investigators found that a "fraudulent commitment letter was generated and forwarded via WhatsApp" text message to supply the government with personal protective gear valued at 23.7 million rand ($1.5 million).

Another showed that a director at one of the companies investigated was related to a senior ruling ANC official and former cabinet minister who served under scandal-tainted president Jacob Zuma.

The company was awarded a contract to supply 200,000 bars of soap, but the SIU established that "no competitive bidding process was followed in awarding the contract".

The SIU has already started recovering some of the funds.

Early this month Ramaphosa received the first instalment of a long-awaited report into corruption at the heart of the state under Zuma.