The NPA withdrew charges against sidelined crime intelligence boss Lt-Gen Richard Mdluli because the case had loopholes, not because it was instructed to do so.
This was the testimony on Friday of the national head of the specialised commercial crimes unit, Lawrence Mrwebi, at suspended National Prosecuting Authority advocate Glynnis Breytenbach's disciplinary hearing.
"At all times... nobody said... advocate Breytenbach must not prosecute Mdluli," Mrwebi said in Pretoria.
"But it must be done properly."
Mrwebi is Breytenbach's senior in the National Prosecuting Authority.
He was asked whether he had been "irrationally" and "blindly" adhering to instructions to drop the case against the former police crime intelligence head, who was being investigated for fraud. He said he found this suggestion offensive, considering prosecutors had to act without fear or favour.
Mrwebi said Breytenbach was free to re-enroll the case against Mdluli any time after she had dealt with the "loopholes" and provide a report on how these had been corrected. He had never received the report.
Prosecutor in the hearing William Mokhari SC said Breytenbach had made it known throughout the NPA that she was unhappy with Mrwebi's decision.
Details of the controversy had also been leaked to the media, he said.
Mrwebi said although there was a lot of "noise" about Mdluli's charges being withdrawn, there was nothing said about his co-accused, who also no longer faced charges.
There had been accusations that Mdluli was being protected because of his political links, which reportedly went as high up President Jacob Zuma.
Mrwebi said he had told Breytenbach at a meeting on December 9, 2011 with her colleague Sibongile Mzinyathi, to fix the loopholes, and re-enroll the case in line with constitutional expectations, among other things.
Some of the evidence they had was inadmissible, he said.
"Glynnis, you don't have to ask permission. By all means, once the investigation is complete please re-enroll and proceed with it," he said.
Breytenbach faces various charges of misconduct, including allegedly failing to act impartially in an investigation relating to a mining rights dispute between Imperial Crown Trading (ICT) and Sishen/Kumba Iron Ore.
ICT lawyer Ronald Mendelow laid a complaint against her handling of the investigation against ICT and Kumba. The case against Mdluli was provisionally withdrawn on December 14, 2011. The mining dispute itself would be heard in an appeal court next month.
Mrwebi said he had nothing to do with Breytenbach's suspension.
"Well, I was not involved in any suspension procedure," he said in reply to questioning by Mokhari.
National Director of Public Prosecutions Nomgcobo Jiba suspended Breytenbach last April.
Earlier, he said it was unheard of and against the NPA's code of conduct for complainants to help prosecutors with their investigation.
"It's when you lose your objectivity, you can't do it," Mrwebi said.
One of Breytenbach's misconduct charges relate to her and Kumba lawyer Michael Hellens drawing up affidavits and warrants together, which ICT complained about.
There is nothing wrong with helping the complainant or their counsel lodge the complaint, but "that would be the end of the matter for that complainant", he said.