South Africa's reaction to the crash was very slow and suspicious. The South African officials relayed false information to the Mozambican authorities. It took them nine hours to report the incident in spite of Mozambique Minister of Security reporting the plane missing. When news of the crash was communicated to Mozambique, it was reported that the crash had taken place in Natal, some 200 kilometres away from the actual site of the accident.
A few days after the crash, Mozambique and South Africa agreed to establish an International Commission of Inquiry (ICI) with the participation of the International Civil Aviation Organization (ICAO) and in line with to ICAO procedures. According to the ICAO (also known as the Chicago Convention), the procedures dictated that South Africa should lead the investigation process as it was the country where the crash occurred. The procedures also dictated the inclusion of Mozambique, as the owner of the aircraft and of the Soviet Union as the manufacturer. In compliance with these procedurers the South African government thus instituted the Margo Commission under the chairmanship of Justice Cecil Margo to conduct investigations. The Morgo Commission sat and heard evidence at the Rand Supreme Court in Johannesburg from 20 - 28 January 1987. Mozambique and the Soviet Union withdrew from the investigation from the Commission, accusing the South Africa government of refusing to treat them as equal partners in the investigation.
The investigation were stalled for several weeks as a result of General Lothar Neethling's refusal to make the cockpit voice recorder (the black box) available to the Commission. He had seized it at the scene of the crash. Colonel Des Lynch, who headed the police investigation, told the Commission that it took a letter from a lawyer to persuade Neethling to release the box to the investigators. Based on the evidence gathered from the black box, the Margo Commission concluded that the aircraft was airwothy and fully serviced and that there was no evidence of sabotage or external forces involved. It held the Soviet Crew responsible, claiming that the plane had locked onto a VOR (very high frequency omnidirectional radio), which they had mistaken for Maputo.
It unanimously determined that the cause of the accident was that the flight- crew failed to follow procedural requirements for an instrument let-down approach, but continued to descend under visual flight rules in darkness and some cloud without having contact with the minimum safe altitude and minimum assigned altitude, and in addition ignored the Ground Warning Proximity alarm.'