It said the possibility of a false beacon and the absence of a warning from the South African authorities had not been cleared up and required further investigation.
A total of 25 people died on October 19, 1986, when Machel's presidential aircraft crashed in mountainous terrain south of Komatipoort. A South African investigation blamed the accident on a pilot error, while a Soviet team found that a decoy beacon had caused the plane to stray off course.
The TRC said its own probe did not find conclusive evidence to support any of these findings.
"Circumstantial evidence collected, however, question the conclusion reached by the (South African) Margo Commision."
The TRC said Machel warned former Malawi president Hastings Banda to stop his alleged activities in Mozambique about a month before the crash. Malawi was accused of assisting the Mozambican rebel movement Renamo, which was in some quarters regarded as a surrogate of the former apartheid government.
Machel's widow Graca told the TRC that an earlier threat by Machel to close Malawi's access to the sea was believed to have prompted the Malawi government to consider the possibility of assassinating Machel.
"According to Ms Machel, who gave a moving testimony, this proposal was later put to President Banda," the TRC said.
"The following week, Banda dispatched his senior officers to South Africa for a meeting with (former) President PW Botha, who sent back a message of solidarity."
There was no doubt that Machel was under great pressure at the time of his death.
"Ms Graca Machel confirmed previous attempts on his life, attacks on his residences and attempts by South Africa to attack the Mozambican capital," the TRC said.
It also found evidence that a large number of South African special forces troops converged in the Komatipoort area on the night the crash.
A former Military Intelligence officer testified that senior officers held a braai at an MI base, Skwamans, near Komatipoort the day before the accident.
He said they left in a small plane, and some returned after Machel's aircraft had crashed.
"In a sworn statement, he provided the names of (former defence force chief) General Kat Liebenberg, (former) Foreign Minister Pik Botha, and General van der Westhuizen of MI."
An independent source confirmed that Skwamans was closed shortly after the accident, the TRC said.