Most of the men were attached to the security services and included high-ranking officers, the former Justice Minister, Adriaan Vlok, and the former Defence Minister, Magnus Malan. Several had been named in reports linking them with a dirty war against the rising power of the African National Congress (ANC).
"The Cabinet took the view that no indemnity from prosecution was acquired or granted in these cases," said the Cabinet Secretary, Jakes Gerwel, speaking after a long and sometimes passionate government meeting in Pretoria.
He said any of those police named could still pursue their applications for indemnity in the courts or through a special Truth and Reconciliation Commission due to be set up soon to settle remaining political injustices from the apartheid era. "The Cabinet was divided over whether the indemnities were kept secret or whether they just did not come to [our] attention," Mr Gerwel said. Their existence was only discovered last week by an outraged Justice Minister, Dullah Omar, himself the target of an assas sination attempt in the 1980s when South African agents switched his heart pills for poison.
But Mr Gerwel said the controversy was no threat to the government of national unity, which took power after last April's first multi-racial elections and is due to hold office until 1999.
Ordinary South Africans have not come out on to the streets over the debate. But liberal and black South African opinion has been scandalised by the mere existence of the indemnity offer, seeing the skeleton in the closet as more proof of bad faith by the National Party as it ended its 46 years of white rule.
It also raised the question of just how far the ANC-led leadership can hope to control the more unbending elements of the old Afrikaner-dominated state machine. Already the Truth and Reconciliation Commission seems more likely to sweep past brutality under the carpet.
But after five days of scandal even the National Party switched tack on the amnesty, frightened that the media might do yet more damage to its tarnished image. The Energy Minister, Pik Botha, said on Tuesday that the indemnity applications had only ever been registered, never granted.
Pockets of resistance remained. The outgoing Police chief, General Johan van der Merwe, said that he believed he was still covered by the amnesty, saying he had applied in order to give moral support to fellow applicants who were just obeying orders against "a revolutionary onslaught."
But the collective application for the 3,500 policemen did not specify, as legally necessary, what offences they were seeking indemnity for. ANC militants had to disclose offences when more than 8,000 of them won amnesties during the tortuous negotiations that led up to multi-racial rule. "It was an orchestrated thing, 3,500 applications in the space of four days, even by people who did not ask for it," said Paula MacBride of the lobby group Lawyers for Human Rights. "They were not indemnified against serious offences like murder. But its existence was deliberately withheld.''