President Mbeki set up the Hefer commission
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A former South African minister has told an inquiry that the director of public prosecutions was probably an agent for the apartheid government.
Former Transport Minister Mac Maharaj said he received the information about prosecutor Bulelani Ngcuka in 1989 or 1990 as white minority rule was ending.
President Thabo Mbeki set up a judicial inquiry whilst Mr Ngcuka was looking into alleged government corruption.
After investigating Deputy President Jacob Zuma,
Mr Ngcuka said that there was a case against him in connection with a multi-million dollar arms deal but not enough evidence to take him to court.
Mr Zuma angrily said he wanted to clear his name in court and questioned why details of the investigation had been leaked to the press.
The story has been front page news in South Africa.
Scorpions' sting
Some analysts say the inquiry is part of a power struggle about who should succeed Mr Mbeki in the ruling African National Congress.
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BULELANI NGCUKA
Unknown in 1994
Pledged to fight corruption
Secured conviction of Winnie Mandela
Accused of spying for apartheid
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The BBC's Carolyn Dempster in Johannesburg says that Mr Zuma is seen as a potential successor to Mr Mbeki.
ANC insiders say Mr Mbeki does not want Mr Zuma to succeed him.
She says that he did not have to order the inquiry, headed by retired Judge Joos Hefer, as he has access to intelligence reports, which have not been made public.
Mr Ngcuka has spearheaded the fight against corruption, led by the elite Scorpions unit, which our correspondent says has been "singularly successful" over the past five years.
Among others, stalwarts from the ruling African National Congress, such as Winnie Madikizela-Mandela and former chief whip Tony Yengeni have been convicted.
Mr Ngcuka denied being a spy after suggestions that he was agent RS452.
Since then a young female lawyer, Vanessa Brereton, currently living in the UK, confessed that she was that agent.