The cause of the crash is not yet known.
The Civil Aviation Authority said that it was unclear exactly what happened.
A light aircraft, owned by the Civil Aviation Authority crashed two weeks ago, killing Captain Thabiso Tolo, First Officer Tebogo Lekalakala, and Flight Inspector Gugu Mnguni.
The aircraft was tasked to perform flight calibration of navigation aids at the airport.
The national carrier denied claims that it was using unqualified staff to fill in for striking staff.
Comair and SAA grounded some planes operating between Cape Town, Johannesburg and Durban. Following two days of flight disruptions and aircraft groundings, Transport Minister Fikile Mbalula said things were now back to normal.
The company decided to ground its flights on Monday after an Ethiopian Airlines passenger jet bound for Nairobi crashed minutes after take-off on Sunday killing all passengers on board.
This follows another South African Civil Aviation Authority resolution earlier this month to ground the carriers' flights, citing safety concerns.
The organisation took the decision to cancel flights after it found a lack of maintenance, unreliable emergency services and poor infrastructure in and around the airport.
The South Gauteng High Court on Tuesday ruled that the domestic airline can resume flights, following a South African Civil Aviation Authority decision to ground its operations.
SACAA’s aviation safety executive Simon Segwabe says the latest issue relates to the company not having a flight operations manager.
The plane crashed into a factory, critically injuring three people, one of whom succumbed to their injuries on Wednesday.
The aviation authority says that the investigation is still at an early stage and some details are yet to be verified but a preliminary report will be issued within 30 days of the accident.
Fedusa says it will appeal to Public Enterprises Minister Pravin Gordhan to provide emergency funding.
The airline, however, already has a 10-year contract to receive Jet Fuel from South African Airways (SAA).
The SACAA announced on Thursday that it had suspended the carrier’s operating license with immediate effect.
The decision means that the carrier may no longer operate with immediate effect. The SACAA says it found serious non-compliance of airline maintenance organisation which poses a serious safety risk.
Questions from Eyewitness News prompted the probe after obtaining correspondence which revealed complaints about inadequate training at a CAA accredited service provider.
