"They are interested in horse trading, and are asking for things I cannot gaurantee," he told Sapa.
These included assurances from the commission that they would be immune from prosecution in neighbouring countries and that their legal costs would be fully covered.
At a recent meeting with senior commission officials, former police commissioners Johan van der Merwe, Mike Geldenhuys and Johan Coetzee undertook to provide details of about 50 incidents of politically-motivated abuses.
Van der Merwe said on Friday that if no agreement was reached as to who would cover legal costs, it would be "very hard" for the generals to go ahead with their submissions, in particular those detailing incidents of gross human rights abuses in which policemen were involved.
Ntsebeza downplayed reports that the commission was at loggerheads with Deputy President Thabo Mbeki after he apparently intervened to stop the commission from issuing subpoenas to the generals.
"I don't know if we are making a mountain out of a molehill. In the main the relations between the commission and the government are very good," he said.
While he accepted that Mbeki had acted in good faith, the commission's timing had been disrupted because the generals would now be able to examine the testimony of convicted murderer, former security policeman Col Eugene de Kock ahead of testifying.
The commission had lost the advantage of having them testify first, he said.