An aircraft, chartered by the prominent Gupta family, which has close ties to President Zuma, landed at the restricted Waterkloof Air Base in Pretoria on Tuesday.
The aircraft carried about 200 people en route to Sun City for the wedding taking place this week.
The foreign ministry's chief of protocol Bruce Koloane was placed on leave pending an investigation into the incident.
International Relations spokesperson Clayson Monyela said preliminary investigations show no permission was given for the airplane to land at the military airbase, state-owned broadcaster SABC reported.
"There was no executive authority granted either by the Department of international Relations, the Presidency and indeed the Department of Defence. However, having said that, some government officials in the process managed somehow, to secure flight clearances and thats what the preliminary reports shows us," Monyela said.
"And that's why this decision has been take so that all these matters can be probed around circumstances in which they were able to secure this flight clearance allowing this plane to land there, when it should not have because that's a military facility, no civilian plane should be landing," he said.
Local radio reported that the Guptas' wedding guests were flown to the base and escorted from there by blue-light vehicles to Sun City, in North West.
The billionaire family, which owns The New Age newspaper and Sahara Computers, is expected to celebrate the wedding of Vega Gupta, 23, to Indian-born Aaskash Jahajgarhia at Sun City between May 1-4.
The wedding, billed as 'the South African wedding of the century', also has Bollywood actors and singers flying in for an extravagant celebration.
On Wednesday, the Gupta family said permission to land at Waterkloof was obtained through the Indian High Commission.
They said the High Commission had applied for permission for the plane to land at the base, because the delegation included government ministers.
Meanwhile, the minister in the Presidency Collins Chabane said that President Zuma is not going to attend the lavish Gupta wedding at Sun City this weekend.
A South African National Defence Force spokesperson said earlier he was not aware of permission being given to any private citizen to land at Waterkloof. The Tripartite alliance has called for a probe into the incident.
The Gupta family has booked the entire resort, even as a public outcry intensifies over granting the family permission to land at the Waterkloof military base in Pretoria. Chabane said invites were extended to some members of cabinet.
Cabinet has meanwhile, refused to comment on the Gupta aircraft landing.
Image: South Africa's President Jacob Zuma
Photograph: STR New / Reuters
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