A former head of Rwanda's external intelligence service was found strangled in a hotel in South Africa, where he has lived in exile for several years, his opposition party said.

"The Rwandan opposition is deeply saddened to announce the assassination of Colonel Patrick Karegeya in Johannesburg," the Rwanda National Congress (RNC) said in a statement on Thursday.

"His body was found in a hotel where he went for a meeting."

"It is true," Frank Ntwali, the party's chairman for Africa told AFP news agency.

"He was strangled by agents of [Rwandan President Paul] Kagame."

Ntwali said Karegeya was killed at the Michelangelo Towers, an upmarket hotel in the Johannesburg suburb of Sandton. It was not immediately clear if he was killed on Tuesday night or on Wednesday.

Karegeya, in his early fifties, was for a long time very close to Kagame.

He served as head of external intelligence for around a decade before being demoted to army spokesman and was later arrested and jailed.

He was stripped of his rank of colonel in 2006 and fled into exile the following year.

Another prominent Rwandan dissident in South Africa, Faustin Kayumba Nyamwasa, survived two assassination attempts in June 2010.

Rwanda accused Nyamwasa of terrorism and trying to destabilise the country.

The RNC statement said investigations had found "overwhelming evidence of the involvement of Rwandan intelligence operatives in those attempts".

Rwanda has vehemently denied involvement in the attacks.

Karegeya and Nyamwasa are both prominent figures in the opposition party, despite not holding specific posts.

Karegeya leaves behind his wife Leah and three children.