The cabinet minister responsible for the State Security Agency, Ayanda Dlodlo, has fallen out with two of her top spies.
One of the spies is Sam Muofhe, the head of the domestic spying branch and an old friend of President Cyril Ramaphosa.
The cause of the fallout is said to have been over the intelligence agency's failure to anticipate the xenophobic violence that erupted in Gauteng last month.
Dlodlo complained about the shoddiness of intelligence she received from Muofhe after the killing of a taxi driver in Pretoria, and looting and violence targeting immigrants.
The tension between the minister and the spies is likely to undermine efforts to clean up the agency. A high-level panel investigating the agency found evidence of irregular spending and criminal acts that happened during Jacob Zuma's presidency.
The Sunday Times can reveal that Dlodlo wrote to Muofhe on September 4 asking him why she should not take action against him for the poor quality of his reports. She demanded an urgent plan from him to deal with the violence.
"This has significantly disempowered me to fulfil my legislative obligations and subsequently put the country and its people under threat and instability," said the letter.
"I further require that you provide me with an explanation as to why I shouldn't take necessary actions as a consequence of your actions," according to the letter.
At a subsequent planning session with top officials of the agency, Dlodlo told the meeting that Ramaphosa was concerned about the lack of intelligence on the violence.
It was at this meeting Dlodlo is alleged to have asked Muofhe and the director-general of the SSA, Loyiso Jafta, to intercept the communications of the suspected kingpin behind xenophobic attacks.
This was after the agency received a tip-off that the man was allegedly planning to raid the businesses of foreigners in Fordsburg and downtown Johannesburg.
Dlodlo was told the interception would require the authorisation of a judge.
Senior officials have accused Dlodlo of issuing instructions to intercept communications without a court order.
Muofhe, who grew up with Ramaphosa in Soweto, declined to comment yesterday.

Last week Ramaphosa summoned Dlodlo after Jafta wrote to him complaining about Dlodlo's alleged illegal instruction.
Jafta is said to have complained to Ramaphosa that Dlodlo was hellbent on reinstating top agency managers loyal to the former director-general, Arthur Fraser.
Dlodlo's spokesperson Mava Scott said the minister was fulfilling her legislative functions.
"It is common cause that in the context of a work environment, there will be different opinions on approaches, strategy and tactics in the implementation of programmes and any other business of an organisation," he said.
When asked about the conflict, Scott said: "The responsibility of the minister is political and strategic oversight and direction while the leadership and membership of the agency have an operational responsibility to provide predictive, responsive, credible, reliable, relevant intelligence on matters affecting national security."
Ramaphosa was also told that Dlodlo was not implementing the recommendations of the high-level panel that investigated the state of the SSA. The panel was led by former cabinet minister Sydney Mufamadi.
In a letter that Dlodlo wrote to Muofhe on September 18, she berated him for the lack of information on the protests and violence around the country. By then, 10 people had died in the violence.
Muofhe is said to have written back, defending himself and calling out Dlodlo for issuing an "illegal instruction".
SSA insiders said the tension between the minister and operational heads Muofhe and Jafta escalated when the minister ordered acting heads of the SSA return to their old positions.
A source in the SSA loyal to Jafta and Muofhe said the clash was a result of the minister interfering in operational matters
In the SSA there are currently eight deputy directors-general but only seven positions in the organisation's structure. In the seven positions only two deputy directors-general are permanent while there are five vacancies, the Sunday Times established.
There are 37 people earning salaries as general managers for 34 positions but there are 25 vacancies that have acting heads.
"The rest are unplaced, displaced or are suspended. This means 27 general managers get paid for nothing," said a source.
Of the 91 manager positions, 48 people are acting while 11 others are paid as managers but do not have positions, according to the source.
But a source in the SSA loyal to Jafta and Muofhe said the clash was a result of the minister interfering in operational matters.
On October 1, Jafta wrote to Ramaphosa seeking his intervention. The president is said to have sided with Jafta and Muofhe, instructing that all top managers in the SSA continue in an acting capacity.
Ramaphosa appointed Dlodlo intelligence minister in June after the elections and appointed Muofhe as head of the domestic branch of intelligence in August. Ramaphosa's spokesperson, Khusela Diko, said he is in regular communication with the minister and operational heads of the SSA.
"The president will however not comment on the details of such engagements except to reaffirm his commitment to the building of a professional national intelligence capability for South Africa that respects and upholds the constitution, and the relevant legislative prescripts," she said.






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