Originally, the charges were dropped weeks before the 2009 election which led to him becoming president.
But last month, a high court judge described that decision as “irrational”. South Africa’s prosecution says it will appeal against a court ruling that it should reconsider corruption charges against President Jacob Zuma.
Mr Zuma has always denied the allegations which are linked to a 1999 arms deal worth billions of dollars.
Judge Aubrey Ledwaba said the National Prosecuting Authority (NPA) should consider re-opening the case.
But National Director of Public Prosecutions Shaun Abrahams said that prosecutors should be able to exercise discretion over whether an investigation should continue.
Briefing journalists, Mr Abrahams said that this was an issue that affected the separation of powers and that the high court’s ruling that the NPA should reconsider the case against Mr Zuma “has far-reaching ramifications”.
He said he would be seeking leave to appeal against the high court ruling at the supreme court.
The opposition Democratic Alliance asked the courts to review the 2009 decision after it got access to the evidence in the so-called “spy tapes” that led the chief prosecutor Mokotedi Mpshe to drop the case.
In 2009, Mr Mpshe said that the tapes – recordings of phone conversations between officials discussing the timing of the case against Mr Zuma – suggested that there was political interference in the investigation.
Last month, Judge Ledwaba said Mr Mpshe had “found himself under pressure” when he decided to discontinue the prosecution and “consequently made an irrational decision”.
“Considering the situation in which he found himself, Mr Mpshe ignored the importance of the oath of office which commanded him to act independently and without fear and favour.
“Mr Zuma should face the charges as outlined in the indictment,” the judge said.