Dumisa Ntsebeza, head of investigations for the statutory Truth and Reconciliation Commission (TRC), said in a statement that a closed investigative inquiry into the crash would be held on 4 June in Cape Town.
"The TRC has been presented with new evidence linking the crash with the activities of the former South African Defence Force," Mr Ntsebeza said.
He said a former SADF military intelligence operative, two other ex-members of the SADF and a former Mozambican official had been invited to give evidence, but their identities were withheld because of fear for their safety.
Mr Machel - who led Mozambique to independence from Portugal in 1975 - and 33 others died in a plane crash over South Africa in October 1986.
Mozambique, then a close ally of the anti-apartheid movement, has never accepted the conclusion of an inquiry, chaired by South African Judge Cecil Margo in 1987, that pilot error caused the plane to crash.
The inquiry ignored evidence that Mr Machel's Soviet-built Tupolev jet was diverted from its correct flight path by a radio beacon transmitting on the same frequency as the one at Maputo airport, its destination.
The South African President, Nelson Mandela, who is companion to Mr Machel's widow, Graca, last year reopened an investigation into the case.