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Doctor Wouter Basson, 49, a heart surgeon at Pretoria's main military hospital, will now not be tried for his alleged part in the murder of 200 detainees held in the former South West Africa, now Namibia.
Prosecutors had charged him with supplying muscle relaxant given to the prisoners in lethal injections before their dead bodies were dropped from aircraft into the Atlantic Ocean.
Poison-tipped umbrella
Judge Willie Hartzenberg also dismissed four other charges of conspiracy to murder, in cases where the actual or attempted murders took place abroad.
One case involved the attempted murder of two members of the African National Congress, Pallo Jordan and Ronnie Kasrils, in London in 1988, with a poison-tipped umbrella and screwdriver.
Both intended victims went on to become members of ANC governments after the end of white minority rule in South Africa in 1994.
Tainted beer
Other cases involved the murder of ANC soldiers in Swaziland and Mozambique, some of them with tainted beer.
Judge Hartzenberg ruled South African courts cannot judge offences committed abroad and that Dr Basson was covered by a 1989 amnesty declared in Namibia.
He adjourned the case until October 25, to allow the prosecution time to appeal or amend the indictment.
Prosecutors had charged Dr Basson with conspiracy to murder, rather than actual or attempted murder, on the grounds that the killings were plotted and the poisons were prepared in South Africa.
Judge Hartzenberg also dismissed a charge of intimidation involving allegations that Dr Basson supplied a baboon foetus to hang on the gate of Nobel Peace laureate Archbishop Desmond Tutu's house in 1989.
The doctor still faces 61 charges, including 16 of murder, eight of conspiracy to murder, and 24 of fraud. But correspondents say that if Judge Hartzenburg's ruling stands then some of the most chilling details of the apartheid state's alleged murder techniques will not be heard during the trial.
Dr Bassoon has yet to plead, he has refused to seek an amnesty from Archbishop Tutu's Truth and Reconciliation Commission.
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