The ministry of justice expressed concern at the revelation by Machel's widow Graca at the South African Truth and Reconciliation Commission (TRC), that the former Malawian government of late dictator Kamuzu Banda was connected to the death.
In a statement Malawi said it would not shield any person who may have contributed directly or indirectly to Machel's death.
Local media quoted Graca telling the TRC that she had no doubt her husband died in a conspiracy involving agents from Mozambique, Malawi and South Africa.
The Banda regime did not enjoy a good relationship with Machel, who at one time threatended to plant bombs along their shared border accusing Malawi of harbouring RENAMO insurgents who waged a 16-year war with Mozambique.
Machel and 34 others were killed when the Tupolev plane in which they were travelling from Zambia to Mozambique on October 19, 1986 crashed into a mountain on the South African side of the border with Mozambique.
The TRC wants the South African government to reopen an investigation into the mysterious crash, which a 1987 inquiry blamed on pilot error.