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Free State director general Elzabe Rockman signed a three-year contract to redesign the website in 2011.
She had reportedly disputed the amount, claiming it was actually R40m.
The agreement was signed with businessman Tumi Ntsele, who reportedly holds tenders with several other provincial departments.
It was reported that the company was awarded the tender even though two other companies submitted significantly lower bids.
Etionee Bruwer, owner of web development company Jam Factory, told the newspaper the amount charged for the website was "ridiculous".
"The company that is working on that site is probably making R3.5m profit a month," he said.
Bruwer said the most paid for a website was R12m, by financial institutions which needed to protect sensitive information.
Ntsele told the newspaper opposition parties had an agenda against black businessmen and that the website's cost was fair.