The NPA's reputation has taken a hammering after the Lonmin killings, despite it having provisionally withdrawn the murder charges against the miners.
The NPA is also facing leadership challenges because the acting national director of public prosecutions, advocate Nomgcobo Jiba, is going on maternity leave soon.
Senior NPA sources told the Mail & Guardian they believe Jiba would have been consulted by the director of prosecutions for North West, advocate Johan Smit, before charging the 270 miners with murder at the end of last week.
Although on paper the regional head would make such a decision, in practice it was done in consultation with the national director of public prosecutions, they said. The murder charges were considered a "bad idea" by those with lengthy prosecution experience, the M&G was informed.
At a press conference last Sunday to announce that the NPA was provisionally withdrawing the murder charges against the miners, Jiba made it clear Smit had taken the decision to charge them.
But senior NPA sources said her stance in hanging Smit out to dry just reflected the lack of leadership at the NPA and it now appeared to be a political decision about who is appointed to the key post of national director of public prosecutions.
The NPA would have to find someone to stand in for Jiba – already acting in her position – in the near future because she is pregnant, NPA spokesperson Bulelwa Makeke confirmed. "We do not know who is going to replace her and I cannot tell you when she is going on maternity leave. You are getting way ahead of things."
It was revealed in April this year that President Jacob Zuma had expunged the criminal record of Jiba's husband, Booker Nhantsi, two years ago. A former lawyer and Scorpions member, Nhantsi's criminal record for stealing a client's money from his trust fund was erased in September 2010.
Jiba was appointed deputy national director of public prosecutions in January 2011 and acting head of the NPA at the end of last year after the Supreme Court of Appeal found Zuma's appointment of Advocate Menzi Simelane was irregular.
Simelane is still on special leave, remaining in his post on full pay until the Constitutional Court passes judgment on the appeal court's December 1 ruling.
The NPA has come under fire for questionable decisions it has taken in recent months, including the suspension of the head of the specialised commercial crime unit in Gauteng, Glynnis Breytenbach.
Whereas the NPA has claimed that her suspension is related to her alleged abuse of power in the Kumba-Imperial Crown Trading case, Breytenbach has argued in the Labour Court that the NPA had "ulterior motives" when it suspended her. It was to prevent former crime intelligence chief Lieutenant General Richard Mdluli from being prosecuted for fraud and corruption, she claimed.
The latest upheaval for NPA staff came with the news that the miners were to be charged with murder. ANC treasurer general Mathews Phosa called the charges "absurd" and there was an outcry around the world.
The legal team acting for the miners, led by advocate Dali Mpofu, had no prior warning that they were to be charged with murder and only found out about it in court last week.
The NPA swiftly called a media briefing after Mpofu's team sent a letter to Zuma, demanding that the miners be released by Sunday. Zuma responded by saying he could not release them, but the team told the M&G they "read between the lines and knew something was about to happen".
Asked whether he was the fall guy for the fallout from the controversy around the charges, Smit said he stood by what he had said at the press conference.
Sharing a platform with Jiba, Smit explained why he was going for the murder charges, based on the legal principle of "common purpose". He pointed out that the murder charges related to the killing of 34 protesters and compared it to other legal precedents, describing his decision as "sound".
The murder charges have been provisionally withdrawn and Smit confirmed they could be reinstated if it was considered necessary. He said the miners have now been charged with "public violence, attempted murder and possession of weapons".