Following the demise of the apartheid regime in 1994, the newly elected democratic government opened new probes into the death of the former Mozambican president, Samora Machel. The Truth and Reconciliation Commission (TRC), which was instituted in 1996 under the chairmanship of Archbishop Desmond Tutu, was tasked to contribute to the investigations. It called everyone suspected of being involved in the plane crash, and those had close ties with Machel in Mozambique Some of the suspects called by the TRC were senior government officials and officials attached to the government security institutions.

The TRC's investigation did not find any conclusive evidence to support either of the earlier reports. Circumstantial evidence collected did, however, bring into question the conclusions reached by the Margo Commission. For example, a police video in the TRC's possessiont shows the South African Foreign Minister Roelof "Pik" Botha telling journalists at the crash site that President Samora Machel and others killed in the crash were his and President P. W. Botha's very good friends, and that their deaths were therefore a tragedy for South Africa.

The TRC report concluded that the questions of a false beacon and the absence of a warning from the South African authorities require further investigation by an appropriate structure.

In his State of the Nation address on 3 February 2006, South Africa's state President Thabo Mbeki announced that there would be a commemoration of the 20th anniversary of Samora Machel's death. In his parliamentary report, the Minister of Safety and Security, Charles Nqakula, said that South Africa, together with its Mozambican counterpart, would resume investigations into the death of Samora Machel. "We owe it to the people of Mozambique to ensure the matter is thoroughly investigated." He added: "Discussions are underway for dealing with the matter."

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