Foreign affairs deputy minister Aziz Pahad has resigned, the department announced on Saturday.

"I have come to this decision after concluding that Judge Nicholson's judicial activism has led him to conclude that the then President [Thabo] Mbeki and his entire cabinet interfered politically in the work of the National Prosecuting Authority," Pahad said in a statement.

He said these were serious allegations "which asserts that we have collectively violated the constitution and acted illegally and criminally and therefore liable for prosecution".

"Given this reality my principles, convictions and conscience will not enable me to serve in the executive."

According to Pahad Mbeki's cabinet unanimously agreed to lodge an appeal against Nicholson's assertions.

"The former president has lodged an appeal against some aspects of Judge Nicholson's judgement and until the constitutional court pronounces on this appeal, I and indeed the entire previous cabinet will continue to live in the shadow of doubt and suspicion," he said.

He said this was a "very difficult and emotional" decision to take after having spent 52 year in the freedom struggle, in which 15 years was in government.

"Due to unfortunate communication problems, President [Kgalema] Motlanthe on Thursday announced that I had been re-appointed as Deputy Minister of Foreign Affairs."

"While I am delighted and honoured that the President has once again showed confidence in my ability to be an active and useful member of the Cabinet collective, I have written to the President to inform him that I am unable to accept his decision," Pahad said.

He said he remained a loyal member of the African National Congress. He would continue to give Motlanthe and the government all support in their endeavours to achieve a better South Africa, a better Africa and a better world.

Sapa