Former Rwandan spy chief Patrick Karegeya murdered in Johannesburg

Former Rwandan spy chief Patrick Karegeya who has been found murdered in Johannesburg (AP)

An exiled former Rwandan intelligence chief has been found murdered in a Johannesburg hotel room.

Patrick Karegeya, 53, who had been granted asylum in South Africa, appears to have been strangled.

He fled Rwanda in 2006 after he fell out with President Paul Kagame, and Rwandan dissidents have accused the President of ordering his assassination.

The suspicious death of Karegeya, a former Kagame ally who turned against him, follows a pattern of assassinations ordered by the Rwandan president, said Theogene Rudasingwa of the opposition coalition Rwandan National Congress. Kagame's government vehemently denies it has targeted dissidents.

Karegeya's body was discovered in a room at Johannesburg's plush Michelangelo Towers hotel on New Year's Day, and many questions remain unanswered in a country with a high crime rate.

"He was found in the hotel room dead on the bed," said a statement from South African police spokeswoman Lt. Col. Katlego Mogale. "A towel with blood and a rope were found in the hotel room safe. There is a possibility that he might have been strangled." She said a murder investigation has been opened in the death of the 53-year-old who reportedly fled to South Africa in 2007.

Karegeya, the former Rwandan intelligence boss, said in a conversation on 30 November with an AP journalist that he understood that his organising of opposition to Kagame was risky and could cost him his life. Karegeya said his family was being persecuted: his daughter's Rwandan passport was revoked on Kagame's orders while she was trying to leave Uganda, where she grew up in exile, and his own quest for work with the United Nations had been obstructed by Kagame.

Kagame's spokesman and Rwanda's foreign minister could not be reached by telephone and did not immediately respond to email requests for comment.

AP