South Africa, already embroiled in the most bitter political crisis since the end of apartheid in 1994, was thrown into further confusion yesterday after President Mbeki suspended the chief prosecutor for failing to pursue the President's rival.

Mr Mbeki’s surprise decision to suspend Vusi Pikoli, citing an “irreversible breakdown of relations” with the Justice Minister, shocked opposition figures. Analysts said that the move was evidence of a power struggle over the prosecution of the former Vice-President, Jacob Zuma. It came after weeks of reported friction between Mr Pikoli and Brigitte Mabandla, the Justice Minister, over the prosecution of Mr Zuma.

Mr Mbeki fired Mr Zuma, 65, after his financial advisor and close aide was named in a multi-million pound arms corruption scandal. Similar charges against Mr Zuma collapsed on a technicality.

The National Prosecuting Authority (NPA), a nominally independent body which controls South Africa’s FBI-style Scorpions unit, was charged with revisiting the dossier. NPA sources say Mr Pikoli was inclining to the view that new charges would not stick.

Supporters of the President, who are deeply opposed to a Zuma candidacy, argue that if he faced chargers, it could wreck his credibility as a serious contender for the ANC leadership.

Mr Zuma, a popular grassroots politician, is still the ruling African National Congress’s deputy president, and a leading contender to be the ANC’s next president at a congress in December. The ANC’s president will be the party’s candidate at the next presidential poll in 2009 - a prospect which terrifies the anti-Zuma camp.

Mr Mbeki, who has to stand down after two terms in 2009, has nevertheless indicated that he would accept a third term as the ANC leader, but in recent months he has lost ground to Mr Zuma who last year successfully challenged rape charges his supporters say were politically motivated.

Ms Mabandla has said publicly that the police “are the superior crime-fighting force” - raising fears that the NPA could fall victim to South Africa’s increasingly polarised politics.

Helen Zille, the leader of South Africa’s main opposition Democratic Alliance (DA) party, said that the suspension of Mr Pikoli, 49, was a “serious development” that needed further explanation.

“The country needs to know why Pikoli has been suspended,” she said, adding that her party would call on parliament’s justice committee to discuss the issue.

Mr Mbeki also recently fell out with his former spy chief as a result of the bitter infighting which has broken over “the Zuma affair”.

Mr Zuma, who spent ten years as a political prisoner on Robben Island alongside Nelson Mandela, has impeccable struggle credentials and has cast himself as the champion of poor, township blacks who have not benefited from Mr Mbeki’s free-market economic policies.

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