The 44-year-old former security police lieutenant-colonel is on R50,000 bail pending appeal against a 20-year jail sentence.
He was convicted in June this year of the Motherwell car-bomb killings in which three policemen and an informer were killed in 1989.
Other policemen convicted in the Motherwell trial, Brig Wahl du Toit, 45, commanding officer of the security police's technical unit in Pretoria, and Maj Martiens Ras, 34, a former Vlakplaas hit-squad operative, are also applying for amnesty along with another former policeman, Gerhard Lotz of Port Elizabeth.
A reliable source close to Nieuwoudt said last night he would be applying for amnesty in three cases - the Motherwell car-bomb killings, the Pebco three disappearance and the 1982 death of Siphiwo Mtimkulu.
"Gideon will definitely not be applying for amnesty for the murders of the Cradock Four, he had absolutely nothing to do with that," the source said.
"He is definitely not paranoid to keep his application secret."
Nieuwoudt's lawyer Francois van der Merwe last night said his client categorically denied any involvement in the Goniwe killings.
He said while Nieuwoudt was considering applying for amnesty nothing had been finalised yet and no application filed with the commission yet.
The burnt and mutilated bodies of Cradock activists Matthew Goniwe, Fort Calata, Sparrow Mkhonto and Sicelo Mhlauli - later dubbed the Cradock Four - were found in the bushes at Bluewater Bay on June 27 1985.
The three members of the PE Black Civics Organisation - Sipho Hashe, Champion Galela and Qaqawuli Godolozi - known as the Pebco Three, disappeared from Port Elizabeth airport in 1985.
They were apparently later taken to an isolated police station near Cradock where they were tortured and later killed.
Mtimkulu was allegedly poisoned and later died. In June this year Nieuwoudt twice got a Supreme Court interdict preventing Mtimkulu's mother Joyce from giving evidence at Truth and Reconcialtion Commission hearings about the poisoning and death of her son.
The source said Nieuwoudt would not be applying for amnesty for the alleged torture of Eastern Cape saftey and security MEC Dennis Neer. Nieuwoudt is in the process of preparing civil action against Neer, according to the source.
Neer named "notorious Nieuwoudt" as one of his interrogators when he was detained and tortured after attending the funeral of the Cradock Four.
Van der Merwe said he was not only advising Nieuwoudt on applying for amnesty. He has about 10 other clients seeking advice about applying for amnesty regarding several incidents.
He refused to divulge details.