Zuma has endured months of criticism and growing calls for him to step down after a series of corruption scandals and as the country battles falling economic growth and record unemployment.
National Prosecuting Authority (NPA) director Shaun Abrahams announced the decision to challenge a High Court order to reinstate 783 charges against Zuma, but denied any political pressure.
The charges, relating to a multi-billion dollar arms deal, were dropped in 2009, clearing the way for Zuma to be elected president just weeks later.
But the Pretoria High Court last month dismissed the decision to discontinue the charges as "irrational" and said it should be reviewed by the NPA.
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"The judgement affects... The discretionary powers of the prosecutor," Abrahams told a press conference on Monday.
"It is so important that I believe it needs a decision of an appeal court."
Abrahams railed against suggestions that the NPA was reluctant to prosecute Zuma.
"I will always do what is correct, irrespective of whether the individual concerned is an ordinary citizen, a cabinet minister or a sitting president," he said.