Opposition parties have rounded on President Kgalema Motlanthe, accusing him of putting the interests of the ANC before those of the country in deciding to axe National Prosecuting Authority (NPA) chief Vusi Pikoli.

The commission of inquiry into Pikoli's fitness to hold office had recommended that the NPA boss be reinstated.

The commission, chaired by former parliamentary speaker Frene Ginwala found the government had failed, in its submissions to the inquiry, "to demonstrate that Pikoli is no longer fit and proper to hold office".

In reaching his decision, Motlanthe relied on Ginwala's adverse findings about Pikoli's understanding of the responsibilities of his job - particularly her comment that anyone holding the position of National Director of Public Prosecutions must have "an appreciation for and sensitivity to matters of national security".

Democratic Alliance leader Helen Zille said Motlanthe had "failed the first real test of his presidency, which was to put South Africa's interests before the narrow interests of the Zuma faction of the ANC".

"President Motlanthe's decision to fire advocate Pikoli without justifiable explanation has all the hallmarks of a cover-up. The president has … used (the) findings selectively in the pursuance of a narrow political agenda," Zille said.

She suggested Pikoli had been fired so he could be replaced by a prosecutions boss "who will do the ANC's bidding", particularly in respect of the prosecution of ANC president Jacob Zuma.

"Pikoli has been a great disappointment to the ANC, who believed the party's interests would be protected by the deployment of an ANC member to the position of National Director of Public Prosecutions *1," Zille said.

United Democratic Movement leader Bantu Holomisa said: "It is clear that people are sent to head institutions to promote and protect the ANC, but the moment such people show any backbone, integrity or independence they are hounded out of office."

Only a "depoliticised" civil service would ensure the best people were appointed to senior positions in government.

Holomisa questioned why the government had spent millions of rands on the inquiry only to ignore its findings - as it had done with the Khampepe commission of inquiry into the future of the Scorpions and the Slabbert Commission's report recommending changes in the electoral system.

Independent Democrats leader Patricia de Lille said it was "unacceptable" that the president had decided to relieve Pikoli of his duties after the Ginwala inquiry had found "he carried out his duties without fear or favour".

"Saying that Pikoli did not fully understand national security interests does not hold water for the ID. National security is too often used by the ANC as a disguise for the protection of the narrow political interests of the ANC."

African Christian Democratic Party leader Kenneth Meshoe expressed "shock and disappointment" at the decision and warned that Pikoli's dismissal has "very serious implications for the independence of the NPA".

"We are not convinced by the reasons given by President Motlanthe, namely that Pikoli breached national security … National security is clearly a cover-up for the fact that certain factions within the ANC wanted to get rid of Pikoli."

The ACDP, DA, ID and UDM say they will oppose Motlanthe's decision when it comes before Parliament for ratification.

According to the NPA Act, the president must formally communicate his decision to Parliament within 14 days. Parliament then has 30 days to debate it and reach a decision.