He was giving evidence at a sitting of the commission at Moutse, Mpumalanga.
Van Niekerk said it was his opinion KwaNdebele was too poor to take independence and it could be achieved only through tyranny, "Amin-style".
He said the South African Government failed to intervene to solve the problems of the homeland by dissolving the homeland government and appointing an administrator.
The incoporation of Moutse in KwaNdebele in 1986 was aimed at driving the North Sotho-speaking Moutse people from the area and quashing all resistance to independence, van Niekerk said.
He said he was sacked after SA Defence Force Northern Transvaal commander Gen Hans Moller asked him to fax his suggestions on what should be done about the uprising in KwaNdebele, for presentation to the National Security Council.
Van Niekerk's suggestion was that the KwaNdebele constitution be suspended, the cabinet discharged, the parliament dissolved and an administrator named. He suggested plans for independence be put off until the political situation was more acceptable.
"Their response was to withdraw me," van Niekerk said.
He said former SA Police Commissioner Gen Johan Coetzee later told him Minister of Law and Order Louis la Grange issued the instruction for his dismissal.
Van Niekerk recalled how he once sent a memo to la Grange, detailing scores of crimes allegedly committed by KwaNdebele cabinet ministers, but got no response.
The crimes, which victims alleged were committed by Chief Minister S S Skosana, Minister of Internal Affairs Piet Ntuli and two other ministers, included four murders, 30 robberies, 30 assaults and nine cases of malicious damage to property.
Van Niekerk said: "If I was the Minister of Law and Order and I got such a memo, I would have telephoned my commissioner of police (van Niekerk) and asked him if he had enough investigators to deal with these cases."
Van Niekerk said his offices were bugged by the South African security police and he was forced to discuss confidential matters outside, under a tree.
Van Niekerk commented on his relationship with the KwaNdebele government and the vigilante group Mbokodo, which attacked opponents of independence.
He said Mbokodo was a secret organisation with which he had nothing to do. He first learnt of it in newspaper reports.
Skosana was always very short with him, van Niekerk said, and never discussed Mbokodo.
Van Niekerk said he was never involved politically either with the KwaNdebele government or the "comrades".
He said he was entitled to a Mercedes-Benz as commissioner of police, but refused it because he did not want to owe the KwaNdebele government anything.
In his last days as commissioner he refused to go to the offices of homeland cabinet ministers.