Top spy Jeff Maqetuka has acknowledged that South Africa's civilian intelligence structures are in crisis.
Maqetuka, who heads the State Security Agency, met parliament's joint standing committee on intelligence with his executive management and the provincial heads of the domestic intelligence branch three weeks ago.
During the meeting the top brass laid bare the challenges facing the agency, including acrimonious battles with Minister of State Security Siyabonga Cwele that already have claimed domestic intelligence branch head Gibson Njenje.
"There was a broad consensus that all is not well within the civilian intelligence environment and that there exists a perception, both within and outside the intelligence community, that the State Security Agency has entered into a state of crisis and paralysis," Maqetuka told intelligence staff at a meeting he convened in Pretoria two days after his address to parliament.
Insiders at the meeting said Maqetuka had admitted that the state of affairs was contributing to low morale among staff - something that had to be addressed urgently.
"This crisis bodes neither well for the image of the country nor for the image of the State Security Agency as a whole. It has resulted in the premature departure of [Njenje] and contributed to the low morale among agency members and to a general atmosphere of uncertainty," Maqetuka said.
He said parliament had insisted that the crisis be resolved before it started threatening South Africa's security.
"Remedial action, based on an analysis of the crisis, is required by all stakeholders of the civilian intelligence community in order to give leadership to the resolution of this unacceptable state of affairs," Maqetuka told his staff.
Maqetuka is at the centre of a row with Cwele, who wants him and foreign branch head Mo Shaik to leave the agency.
It follows a meltdown in the relationship between the minister and the three intelligence chiefs in what seems to be a repeat of the internal battles that rocked the intelligence world prior to the ANC's Polokwane conference in December 2007.
Njenje has already accepted a deal in which he will be paid out for the remainder of his contract. Behind-the-scenes negotiations are now under way to pave the way for the departure of the two remaining heads, Maqetuka and Shaik.
Tension between Cwele and his intelligence chiefs began shortly after they were appointed by President Jacob Zuma in 2009.
Government officials close to the process said Cwele was unhappy about Zuma's choice of the three men. The minister has since been accused of interfering in their work, sometimes demanding briefings on intelligence issues he should not be privy to as a politician.
Maqetuka is said to have admitted to parliament that the relationship between the minister and the intelligence chiefs was at an all-time low.
State security spokesman Brian Dube refused to comment on Maqetuka's address to staff or his meeting with parliament.
Cecil Burgess, chair of the parliamentary committee, could not be reached for comment.
The Sunday Times has been reliably informed that Shaik could take up a post as South Africa's next ambassador to Canada. It is understood that Shaik has finally relented to an offer of a diplomatic posting after initially fighting attempts to facilitate his departure from the agency .
Contacted for comment on Friday, Shaik said he was "not aware" of his impending posting to Canada and was still at his desk at the agency.