NPA prosecutor Glynnis Breytenbach's suspension was linked to her probe into former crime intelligence boss Richard Mdluli, her disciplinary hearing heard on Thursday.

"It happened at the same time as matters relating to the Mdluli matter come to a head," Breytenbach's counsel Wim Trengove said.

He said commercial crimes unit head Lawrence Mrwebi and his client had a "heated clash" in November and December last year.

Trengove was cross-examining Hercules Wasserman, acting senior manager of the National Prosecuting Authority's integrity management unit, at the authority's offices in Silverton, Pretoria.

"Advocate Mrwebi... ordered that charges against General Mdluli be withdrawn. Advocate Breytenbach protested that the reasons for the withdrawal were unfounded and that the prosecution should proceed," Trengove said.

On December 14, the charges against Mdluli were provisionally withdrawn.

Breytenbach and a colleague prepared a memorandum in the first half of April challenging the decision to suspend the prosecution of Mdluli.

On April 26, Mrwebi responded, making it clear Mdluli would not be prosecuted.

Mdluli faced a raft of fraud and corruption charges relating to the alleged misuse of a secret crime intelligence fund to buy luxury vehicles. He also faced a charge of murder relating to the death of an ex-lover's husband.

Breytenbach was officially suspended on April 30.

This was after Mrwebi sent a memorandum in mid-January 2012 to acting national director of public prosecutions Nomgcobo Jiba, calling for Breytenbach to be removed from investigating the Sishen/Kumba Iron Ore and Imperial Crown Trading (ICT) mining rights dispute.

She had, however, already been removed on November 25, 2011, following a complaint by Mendelow Jacobs Attorneys, on behalf of ICT, in October that she had failed to act impartially.

Breytenbach was told on February 2 of an intention to suspend her.

Trengove asked Wasserman what had changed between November and February to warrant Breytenbach's suspension.

"On the face of it, it's inexplicable that they should now want her suspended given that there was no reason to do so on 25 November, and nothing has changed since then," Trengove said.

He suggested the only explanation for the turnabout was Mrwebi's memorandum.

Wasserman said he could not comment.

NPA investigators were appointed in early February. Days later Wasserman attempted to get Breytenbach's laptop for analysis.

Wasserman's investigation began in November 2011.

Breytenbach has pleaded not guilty to all 16 charges, which include improper conduct and insubordination, brought against her.

She has contended she was removed in an attempt to protect Mdluli.

The NPA has denied this, and said the suspension related to her alleged misconduct in the ICT investigation.

Jiba banned Breytenbach from communicating with NPA members.

"The effect of what [Jiba] did was to entirely neutralise advocate Breytenbach and her influence in the NPA," Trengove said.

Breytenbach had asked Jiba for a list of witnesses she could not have contact with, but this was not provided.

Trengove asked why Breytenbach was not given adequate time to respond to charges against her, or told in full what she was being investigated for.

After requests from her attorney Gerhard Wagenaar for specific allegations, acting NPA CEO Karen van Rensburg replied in a letter on February 6: "The allegations... relate to the execution of her duties as senior deputy director: public prosecutor in the Kimberley case... the facts of which are within her personal knowledge."

Trengove said there was no way in which anybody could rationally respond to these cryptic allegations.

Wasserman admitted that the first time Breytenbach received some details of the allegations against her was on April 18.

He admitted Breytenbach was not told of the full case against her.

Jiba made the decision to suspend her on April 23. This was despite the fact that Wasserman had given Breytenbach until April 25 to respond to the allegations.

Mdluli was suspended again in May this year, by then acting police commissioner Nhlanhla Mkhwanazi.

Mdluli appealed against his suspension in the Johannesburg Labour Court, but it decided he should remain suspended until he had also filed an application for leave to appeal an interim order – granted by the High Court in Pretoria on June 6, to Freedom Under Law – that he be suspended and not be allowed to do police work.

The hearing will continue at 10 am on Friday.