A private chartered aircraft with a single passenger on board made an unauthorized landing at the OR Tambo International Airport on Wednesday.
A spokesperson for the Transport Ministry Ayanda Allie Paine says the flight from Harare, Zimbabwe landed mid-afternoon.
The passenger, who is an Italian national with a South African passport was not allowed to enter the country and the man and his crew were ordered to leave.
The individual initially refused to leave but after intervention from SAPS the aircraft left the South African airspace on Wednesday night.
Transport Minister Fikile Mbalula has called for a full investigation into the incident.
The Department, working closely with its aviation entities, is reviewing the applicable protocols to ensure that only flights with the necessary approval are allowed to enter the South African airspace.
This requires seamless coordination between the Department of Transport, the Air Traffic Navigation Services (ATNS) and the Airports Company South Africa (ACSA).