Holomisa told Sapa on Wednesday the Promotion of National Unity and Reconciliation Act did not guarantee the safety of witnesses as it merely focused on protection from physical threats.
He was reacting to statements by Truth Commission deputy chairman Dr Alex Boraine that Holomisa's dismissal had created the impression that he had been fired because of his testimony before the commission, in which he renewed allegations of corruption against Public Enterprises Minister Stella Sigcau.
Boraine on Monday said this would make the commission's task more difficult as others might be discouraged to give evidence.
Although President Nelson Mandela and the ANC have refused to give reasons for Holomisa's dismissal, informed sources said it had been a result of a series of "political indiscretions" culminating in Holomisa's testimony and subsequent statements about Sicgau and Deputy President Thabo Mbeki, who intervened in the row.
Holomisa faces an ANC disciplinary inquiry on August 14 where he has to answer to three charges arising from the statements he made to the commission.
Holomisa said he believed the commission ran the risk of losing credibility because of the action taken against him.
"If the commission still wants to be credible, I advise it and government to revisit those clauses dealing with the protection of witnesses."
Holomisa, who was about to leave for Sasolburg on his last assignment as deputy minister, reiterated that he had accepted his sacking.
He again blamed Deputy President Thabo Mbeki for his dismissal and said claims that Mbeki was behind his axing had not been denied.