In a statement released on Thursday, the Special Investigating Unit (SIU) announced Faiek Davids had resigned, effective from the end of the year.
SIU spokesperson Boy Nadala said in the statement: "Family commitments played an important role in his decision and that he wishes to pursue opportunities outside the unit."
Davids took up his post earlier this year, after then acting head of the unit Nomvula Mokhatla reinstated him following a labour dispute that had been ongoing since 2009.
Davids was suspended as the SIU deputy and then fired by the unit's previous head Willie Hofmeyr, after Hofmeyr cited grounds of incompatibility and the "irretrievable breakdown of trust" between the two as reasons for the dismissal.
According to previous news reports, the so-called "Zuma tapes" – intercepted phone calls that played a role in the withdrawal of corruption charges against President Jacob Zuma – were at the heart of the labour issues between Hofmeyr and Davids.
When it was decided to withdraw the charges against Zuma, a small proportion of the intercepted material was released.
Manipulation
The transcripts appeared to show that former Scorpions head Leonard McCarthy had tainted the Zuma investigation by manipulating the timing of the charges to assist former president Thabo Mbeki's bid to maintain control of the ANC.
That conclusion was challenged by McCarthy and former national director of public prosecutions Bulelani Ngcuka, who was also implicated.
Davids took Hofmeyr to the Commission for Conciliation, Mediation and Arbitration (CCMA), for alleged unfair dismissal.
The charges against Davids emanated from a telephone exchange between Davids and McCarthy. This reportedly included a voicemail message left by McCarthy, "presumably" intercepted by the National Intelligence Agency and the police.
However, at the time Davids argued before the CCMA that the conversations were illegally taped. He also denied any misconduct.
It is understood that the conversation cited by Hofmeyr against Davids, allegedly featured McCarthy and Davids discussing an earlier confrontation between Hofmeyr and Ngcuka, who, at that stage, had left the National Prosecuting Authority over Ngcuka's alleged ongoing interference in the Zuma case.
Lost confidence
According to a previous report, after listening to the recording Hofmeyr had lost confidence in Davids's ability to make independent and impartial operational decisions and believed that senior management could no longer work with him.
But earlier this year, Mokhatla announced that "after a careful review of the legal dispute between the SIU and its deputy head Faiek Davids … the parties have agreed to settle this dispute". His reappointment as deputy under the new head advocate Vas Soni was seen to be a "breath of fresh air" for the unit, which has been embroiled in internal battles since Hofmeyr was redeployed.