* Patrick Karegeya found dead, apparently strangled, in hotel room
* Fled to South Africa in 2007 after allegedly plotting coup
* Rwandan opposition party blames Kagame administration (Recasts, adds details)
By Helen Nyambura-Mwaura
JOHANNESBURG, Jan 2 (Reuters) - An exiled former Rwandan intelligence chief was found murdered in a Johannesburg hotel room, police said on Thursday, in a killing a Rwandan opposition party blamed on the country's government.
Patrick Karegeya, who once headed military intelligence in his homeland, fled to South Africa in 2007 after allegedly plotting a coup against President Paul Kagame with former Rwandan army chief Faustin Kayumba Nyamwasa, who was also exiled there.
Karegeya body was discovered on New Year's Day on a bed at Michelangelo Towers, an upscale hotel and apartment complex he had apparently booked in to three days earlier, South African police said.
His neck was swollen and a bloody towel and rope were found in the room's safe, they said.
Paul Ramakolo, a spokesman for South Africa's Hawks, an elite crime fighting unit, confirmed Karegeya had been killed. "We will check if it was as a result of strangulation or what could be the factor," he said.
The opposition Rwanda National Congress, many of whose senior members are also living in exile, described Karegeya's death as an assassination.
"By killing its opponents, the criminal regime in Kigali seeks to intimidate and silence the Rwandan people into submission," it said.
A spokesperson for the Rwandan presidency declined to comment and it was not possible to reach Foreign Minister Louise Mushikiwabo or spokespeople at the Rwandan embassy in Pretoria.
Rwanda's ambassador to South Africa, Vincent Karega, earlier told local radio SAFM he was not aware of details of the killing. "We encourage the authorities to really look into the matter so that we know exactly what happened," he said.
Nyamwasa was shot in the stomach in 2010 as he drove into the driveway of his upmarket Johannesburg home. He survived what his family said was an assassination attempt ordered by Kagame.
Both Nyamwasa and Karegeya, who was 53, fought alongside Kagame in Rwanda's 1994 war, which halted the genocide by ethnic Hutu militia who had killed 800,000 Tutsis and moderate Hutus in just three months.
In 2011, South Africa declined a Rwandan request to extradite Nyamwasa to his homeland. He was also wanted in Spain and France for killings in the 1990s.
Also in 2011, a Rwandan military court sentenced Karegeya, Nyamwasa and two other exiled officers to 20 years in prison for threatening state security after they were tried in absentia. (Additional reporting by Stella Mapenzauswa in Johannesburg and Richard Lough in Nairobi; Editing by Ed Stoddard and John Stonestreet)
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