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Members of the Rwanda National Congress hold pictures of slain party founder Patrick Karegeya, left, and posters of Rwandan President Paul Kagame, right, during a demonstration outside the Rwandan embassy in Pretoria in 2014.ALEXANDER JOE

South African authorities have issued arrest warrants for two Rwandans allegedly linked to the government of President Paul Kagame for the 2013 death by strangulation of a Rwandan dissident in Johannesburg.

The warrants are the latest legal evidence to support longstanding accusations that the Kagame government has used death squads to pursue dissidents in exile. An investigation by The Globe and Mail in 2014 found evidence that senior Rwandan intelligence officials were involved in such plots.

The warrants were issued by a judge at the request of a South African police investigator, according to a letter sent to lawyers for the family of Patrick Karegeya, a former close aide to Mr. Kagame who was killed in Johannesburg after he fled Rwanda and became an outspoken critic of the government.

Police and prosecutors have already stated in earlier documents that they believe the Rwandan suspects have close links to the Kagame government and sought shelter in Rwanda after Mr. Karegeya’s death.

The new letter, signed on Aug. 30 by the director of public prosecutions for the province in which Johannesburg is located, said the local judge had issued warrants for the arrest of Ismael Gafaranga and Alex Sugira, two of the four Rwandans identified as suspects after Mr. Karegeya was strangled to death in the luxury Michelangelo Hotel on Dec. 31, 2013.

“We are still in the process of preparing the papers for the request for extradition,” the letter said. “Once it has been authorized, application will also be made to Interpol for the issuing of so-called ‘Red Notices’ for these two suspects.”

The South African police investigator had applied for arrest warrants for all four suspects, but the judge was only prepared to issue warrants for two of them, the letter said.

Most of the evidence against the suspects was gathered in 2014, but the police delayed the completion of their investigation for several years for unknown reasons. The Karegeya family and its lawyers have suggested it was delayed because it was politically sensitive and would affect diplomatic relations between Rwanda and South Africa.

Late last year, prosecutors called an inquest into Mr. Karegeya’s death, but his family said an inquest would merely waste time, as the suspects were already known. A judge agreed with them and sent the case back to police and prosecutors to make a decision on criminal charges.

At the beginning of the inquest proceedings, the judge disclosed two documents in which South African police and prosecutors said the four Rwandan suspects were directly linked to the Rwandan government. A letter by South African prosecutors last year, for example, said there were “close links” between the Kagame government and the four suspects.

The Globe asked Vincent Karega, the Rwandan ambassador to South Africa, to respond to these allegations, but he declined to comment.

Mr. Karegeya was one of Mr. Kagame’s closest aides for 10 years. He served as the head of Rwandan military intelligence from 1994, when Mr. Kagame’s forces won power after the Rwandan genocide, until 2004. But after a falling out between the two men, he fled into exile and helped found a Rwandan opposition group, the Rwanda National Congress.

Mr. Karegeya’s widow, Leah Karegeya, said she was “extremely happy” at the announcement of the arrest warrants. The case should be “a lesson to the Rwandan government that justice exists in other countries,” she told The Globe.

Kennedy Gihana, a lawyer for the Karegeya family, said the warrants were “an absolutely fantastic victory” for all victims of the Rwandan government.

“I think it sends a clear message to Kagame that the people he sends abroad will be arrested. The independence of the South African judiciary has to be commended.”

He said the two suspects in the arrest warrants were the ringleaders in the assassination of Mr. Karegeya, while the other two were less directly involved.

Gerrie Nel, another lawyer for the family, said the warrants are “a big victory” but are also an indication that South Africa’s National Prosecuting Authority (NPA) had “abused the legal system” by stalling the case for so many years.

“The only feasible conclusion is that the NPA wanted to avoid a prosecution,” Mr. Nel said in a statement.

After the death of Mr. Karegeya and a series of attempted assassinations of another prominent Rwandan dissident, South Africa expelled several Rwandan diplomats in 2014, accusing them of involvement in the plots. But in recent years, Mr. Kagame and South African President Cyril Ramaphosa have been trying to patch up their differences.

Human rights groups have warned that opponents of Mr. Kagame face the threat of unlawful detention, arrest, torture or “disappearances.”

Mr. Kagame himself has made frequent comments that appeared to condone violent attacks on exiled dissidents. After the assassination of Mr. Karegeya, the Rwandan President said, “Those who betray the country will pay the price.”

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