Minister of Agriculture, Forestry and Fisheries Senzeni Zokwana has served preliminary charges on suspended director general Mike Mlengana.
Mlengana was placed on precautionary suspension on June 12 for undisclosed reasons pending an internal probe.
Zokwana on Friday said Mlengana faces charges of "alleged gross misconduct" relating to misappropriation of state funds and failure to comply with the Public Finance Management Act.
"Mr Mlengana also faces charges of alleged insubordination in relation to failing to suspend department officials involved in fraudulent activities; and the contravention of the Marine Living Resources Act."
He also failed to disclose his business partner's alleged involvement in certain department tenders, the minister claimed.
Zokwana said he may add further charges subsequent to the final outcomes of the internal probe.
City Press however reported two weeks ago that Mlengana believed he was suspended because he refused to sign a massive contract for the department.
The contract, with a company owned by two former police generals, was reportedly put in front of him without the proper tender process for contracts in excess of R500,000 being followed.
The suspended director-general told the newspaper he and Zokwana had had a bad relationship for some time, but said he knew he would be suspended when he objected to the minister's decision to award the tender to The iFirm.
Zokwana responded to those comments on Friday, saying he was "disappointed with the false allegations".
"The minister wishes to follow the correct internal disciplinary processes and will therefore not engage on this subject in the media," the ministry said.
Zokwana claimed Mlengana would receive a fair inquiry, and his precautionary suspension have not affected the work of the department.