Defence Minister Nosiviwe Mapisa-Nqakula has ordered that the Gupta family's chartered jet be removed from Waterkloof Air Force Base.
"The clearance should be rescinded and the aircraft should immediately be removed ... ," she said in a statement on Thursday.
The minister further called for an investigation on why the air force was approached with a request to use the base.
She was informed about media reports on the clearance given to the aircraft during her visit to Ethiopia. When she returned on Wednesday she asked for an urgent briefing from the South African National Defence Force (SANDF).
She said the international relations and co-operation department agreed to the Indian High Commission's request for the use of the base.
"The SA Air Force therefore dealt with the request as a normal process that has always applied when [the department] makes such a determination and direction."
Initially a representative from the Gupta-owned Sahara Computers approached the defence department for help with the Indian High Commissioner's request for use of the base.
"This request for assistance was rejected, and since it was not even formalised, the ministry considered the matter closed. It had been our advice that the Airports Company SA was best placed to assist."
She said against expectation, attempts were then made to secure use of the base using diplomatic channels at the international relations department.
The office of the chief of state protocol dealt with the commissioner's request without consulting the chiefs of SANDF or air force, or the defence ministry.
"The ministry of defence and military veterans would never have approved such a request ... ," she said.
On Thursday, the international relations department said the chief of state protocol, ambassador Bruce Koloane, was placed on suspension while it conducted its investigation.
The Gupta family, which owns the New Age newspaper and Sahara, is celebrating the wedding of Vega Gupta (23) to India-born Aakash Jahajgarhia at Sun City, North West. – Sapa