Former spy boss Gibson Njenje has been fired from his position as special adviser to state security minister Dipuo Letsatsi-Duba.

A senior government source told News24 that the minister removed her adviser two weeks ago, ostensibly over alleged irregularities related to a trip to Europe but the same source explained Letsatsi-Duba had grown increasingly suspicious about Njenje's political allegiances.

Njenje told News24 on Friday: "I am not going to deny that, but I am not going to comment any further."

Njenje, the former head of domestic intelligence for the State Security Agency (SSA), became adviser to Letsatsi-Duba in February 2018.

His role was widely seen as being part of efforts to clean up the intelligence agency, although this interference has also irritated some of his enemies – some who remain employed by the SSA.

A high level review panel appointed by President Cyril Ramaphosa to investigate alleged irregularities at the SSA recommended sweeping changes to the intelligence structures earlier this year. In that report, the panel said the intelligence agency was being used in political factional battles, and pointed to instances of alleged financial mismanagement and even criminality. The report was released to the public in March.

During his State of the Nation Address in February this year, Ramaphosa announced he would break the SSA into its two original agencies - foreign and domestic - and the re-establishment of the National Security Council. This was on the basis of the SSA report, he said.

Njenje was seen as a part of these efforts.

On Friday, former spy boss Arthur Fraser responded to the high level panel report, rubbishing much of what the panel found. In that rebuttal, Fraser also said that Njenje began "giving operational instructions to SSA officials" and said he provided "support" to the high level panel.

Njenje, along with two other intelligence heads, Moe Shaik and Jeff Maqetuka were removed in 2011 by then minister Siyabonga Cwele, after raising concerns about the Gupta family.

Njenje also previously served as chairperson to Bosasa, a Krugersdorp facilities management and security company that has been exposed for paying bribes for tenders for nearly two decades. Bosasa also has strong links to the ruling African National Congress (ANC) party and News24 previously revealed the company donated millions to ANC election campaigns.

A spokesperson for Letsatsi-Duba was not immediately available to comment. This story will be updated when a response is forthcoming.