African Eye News Service on Tuesday reported that earlier this year some parts of the missing wreckage were dumped at a scrapyard near White River in Mpumalanga when the Truth and Reconciliation Commission re-opened the inquiry into the crash.
An investigator, director Agrippa Mabuza, on Tuesday said two wheels belonging to the Tupolev jet which killed Machel and 33 others were found on a farm near Komatipoort.
He said: "The farmer said the investigating officers gave him the wheels as a gift but did not disclose why he deserved such a controversial present."
Another bullet-riddled part of the wreckage was found displayed in the pub at Ngwenya Lodge near Komatipoort.
Spokeswoman for the special TRC team investigating the crash, Christelle Terreblanche, said it was unfortunate the wreckage was not being treated with respect.
She said the commission was concerned with testimony that a false beacon was used to cause the plane to crash on a hill-top at Mbuzini on the South African side of the border on October 19, 1986.
She said nine people, including former super spy Craig Williamson, had testified in camera before the TRC on June 3 and 4 and that more testimony were expected before the end of the month.
"The investigation has reached a very sensitive stage. People like Pik Botha, who was then the minister of foreign affairs, have not yet testified."
Mozambican air traffic controller, Antonio Cardoso de Jesus, was suspended on May 5 this year after allegations that South African agents paid him R1,5 million to tamper with the navigational beacon at Maputo Airport on the night of the crash.