By Pascal Fletcher and Helen Nyambura-Mwaura
JOHANNESBURG (Reuters) - South Africa expelled three Rwandan diplomats it linked to a raid by gunmen on a dissident exiled Rwandan general's home and Rwanda ordered out six South African envoys in retaliation, a diplomatic source said on Friday.
Late on Monday, armed men broke into the Johannesburg home of former Rwandan army chief General Faustin Kayumba Nyamwasa, an exiled critic of Rwandan President Paul Kagame.
Nyamwasa, who survived a previous assassination attempt in Johannesburg in 2010, was not in the house at the time.
The source, who asked not to be named, told Reuters South African security services had tracked the attackers. "It was very clear that they were intelligence personnel attached to the Rwandan embassy," the source added.
Three diplomats from the Rwandan mission in Pretoria were ordered out of the country in 48 hours this week. Kigali's tit-for-tat expulsions followed on Friday, the source added.
There was no immediate comment from the Rwandan government.
The diplomatic row was likely to sour relations between South Africa, the continent's largest economy and an influential player in its affairs, and Rwanda, a much smaller state in the heart of the Great Lakes region.
Both countries have been involved in efforts to bring peace to eastern Democratic Republic of Congo, where South Africa has troops in a U.N. brigade that fought last year against M23 rebels whom U.N. experts said were backed by Rwanda. Kigali denied supporting the Congolese rebels.
South African police have also been investigating the New Year's Eve murder in a posh Johannesburg hotel of another exiled Kagame opponent, former Rwandan spy chief Patrick Karegeya.
Exiled Rwandan opposition members have accused Kagame and his government of being responsible for Karegeya's death and for attacks on Nyamwasa and other overseas-based critics.
Kagame and senior Rwandan officials have denied any involvement in the attacks on exiled opponents, but have called them traitors who should not expect forgiveness or pity.
Brian Dube, spokesman for South Africa's State Security Agency, would not comment on the expulsions but confirmed the country's security services had been looking into the attacks against the exiled Rwandans.
The United States in January expressed concern over what it called "politically motivated murders of prominent Rwandan exiles".
David Batenga, a nephew of the slain Rwandan spy chief Karegeya, called for the closure of the Rwandan embassy in South Africa.
"It's not an embassy, it's an operation center for planning missions to kill innocent civilians," he told Reuters.
Etienne Mutabazi, deputy chairman in South Africa of the opposition Rwanda National Congress, of which Karegeya and Nyamwasa were founding members, said the expulsion of the Rwandan diplomats was "long overdue" and called their activities "criminal".
"Diplomats are here to represent their country, they have immunity, but they should not abuse that immunity," he said.
In January, Kagame, who has won Western praise for rebuilding Rwanda after the 1994 genocide there, defended his nation's right to self-defense against those who "betray".
"We didn't do it, but my question is - shouldn't we have done it?" Kagame said at a January 12 prayer breakfast, clearly referring to Karegeya's death but without naming him.
"No one will betray Rwanda and get away with it. Regardless of who you are, there will be consequences," Kagame said.
Karegeya fled to South Africa in 2007 after allegedly plotting a coup against Kagame with Nyamwasa.
(Writing by Pascal Fletcher; Editing by Ed Cropley and Tom Heneghan)