It is mere perception that the National Prosecuting Authority was politically influenced, acting head Nomgcobo Jiba says.
"These are perceptions. We strive to ensure we prosecute without fear, favour or prejudice," Jiba said in Pretoria on Monday.
"That should be applicable to everyone in this country."
Jiba did not elaborate on the issue of spy tapes, which reportedly led to criminal charges against President Jacob Zuma being withdrawn.
"That case is a matter before court."
The acting national director of public prosecutions was speaking at an Institute for Security Studies seminar.
She said the NPA did not withdraw charges against people without reason.
Charges could be withdrawn for a variety of reasons. This did not mean the case had been finalised, and therefore could be brought back to court at a later stage.
"We do not merely withdraw charges against accused people ... there is vigorous consultation and processes to be followed," Jiba said.
"We must take care when deciding to prosecute."
Not trying to defend
She was responding to a Sunday Times report over the weekend regarding the dropping of corruption charges against Zuma in 2009.
She said she was not trying to defend the decisions made by former national directors of public prosecutions (NDPP). However, there were policies in place which had to be followed.
"There will always be some form of unhappiness from the other side [when decisions are made]."
The NPA's decision to drop the charges - taken by then acting NDPP Mokotedi Mpshe - came a month before Zuma was elected president.
The Sunday Times reported that the country's top prosecutors at the NPA were overwhelmingly in favour of pressing ahead with the corruption case against Zuma.
They also dismissed the so-called spy tapes as irrelevant, just days before the charges were dropped.
This was revealed in more than 300 pages of internal e-mails, memos and meetings, the paper reported.
In March, the Supreme Court of Appeal ordered the NPA to hand over a record of all documents, recordings, materials and evidence that led to criminal charges against Zuma being withdrawn. The tapes are yet to materialise.
Prima facie case
Jiba said just because there was a prima facie case did not mean there would be prosecution.
She used the example of a woman who had heard a noise at her window, thought someone was breaking in and shot the person, who turned out to be her husband.
"How do you prosecute something like that?" Jiba asked. "There are instances were there is a prima facie case but you can't prosecute."
Jiba said the NPA was guided by its policies.
Martin Schoenteich, doctoral student at the criminals justice programme at the City University of New York, said the judiciary could not force the NPA to prosecute.
However, the courts could review the processes which had been followed in deciding whether to withdraw charges.
There were other checks and balances; these included Parliament, opposition parties, media and civil societies.
Jiba admitted there were problems facing the NPA, but efforts were being made to improve things.
"We are not sitting around doing nothing. We acknowledge the criticism in the way we measure our performance," she said.
The NPA measured its performance by the number of convictions.
"We have yet to find a perfect system."
Jiba said challenges included the lack of funding to Legal Aid.
"We have noted that there has been a decline in the[ir] performance." – Sapa