South Africa's ruling African National Congress (ANA) said it "noted" Friday's court judgment in Pretoria that the appointment of the country's prosecutions boss, Shaun Abrahams, be set aside.

"The ANC will allow the parties involved to reflect on the judgment and its implications as well as decide whether to appeal or not," the party said in a statement.

"As the ANC, we trust that whatever decision taken will be in the interest of the administration of justice, the National Prosecuting Authority (NPA) and the country as whole."

The court found a settlement agreement with Abrahams's predecessor Mxolisi Nxasana was irregular.

Nxasana was appointed in August 2013 but the very next year faced an inquiry into his fitness to hold office. After first refusing to resign, he left he NPA in June 2015 in exchange for a R17-million golden handshake, which the court on Friday ordered he should be made to repay.

A full bench of the North Gauteng High Court, led by the court's judge president Dunstan Mlambo, also found that it would not be just for the former prosecutions boss Mxolisi Nxasana to be reinstated.

Nxasana said he did not approach Zuma, but the president came to him, implying Zuma had lied under oath in an affidavit that the former national director of Public Prosecutions (NDPP) had left his post voluntarily and had not been forced to do so.

Mlambo ruled it would not be just to bring Nxasana back and at the same time Abrahams could not stay in office.

President Jacob Zuma would not be able to appoint a new NDPP, the court ruled, saying he was "conflicted" given the fact that the NPA was deciding whether to reinstate 783 counts of, among others, corruption, racketeering and fraud against the president after the case was withdrawn in 2009.

The court instructed Zuma's deputy, Cyril Ramaphosa, to appoint a new prosecutions boss within the next 60 days.

It was not clear whether Zuma and his team would apply for leave to appeal the ruling.

The case was brought by Corruption Watch and Freedom Under Law.