South Africa’s prosecutor’s office justified a decision not to pursue four men wanted for the murder of a Rwandan intelligence chief, Patrick Karegeya, on the grounds of “close links” between the suspects and President Paul Kagame’s government in Kigali, a magistrate has revealed.

The revelation by the Johannesburg magistrate Mashiane Mathopa sheds light on the apparent determination by the governments of South Africa and Rwanda to repair relations strained by a series of attacks on Rwandan dissidents who have been granted political asylum in South Africa.

Karegeya, a former presidential aide who founded a Rwandan opposition political party in exile, was found strangled in a room in the five-star Michelangelo hotel in Johannesburg on 1 January 2014. He had gone there to meet a Rwandan businessman friend, one of four men named in the Randburg court last week as possible perpetrators.

Karegeya’s family and opposition colleagues have always blamed the murder on Rwandan intelligence acting on orders from Kagame – a claim he has vehemently denied.

Human rights groups allege Karegeya’s killing appears to form part of a wide-ranging campaign of intimidation and harassment targeting Rwandan opposition politicians, outspoken journalists and civil activists both inside the country and abroad.

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Halting a scheduled inquest into Karegeya’s death in order to give South African police time to explain their failure to prosecute and account for discrepancies in forensic evidence, Mathopa revealed the existence of a previously unseen letter dated 5 June 2018 sent from the prosecutor’s office to the police unit responsible. “The latter letter is of vital importance,” he told the court.

“It reads as thus: ‘The director of public prosecutions remarks as follows: i. After careful consideration of the available evidence, I decline at this stage, to prosecute in this matter. ii. It appears that all the Rwandan suspects left the country in 2014 and returned to Rwanda. Furthermore close links exist between the suspects and the current Rwandan government.’”

The timing of the letter may raise eyebrows. Three months before it was sent, South Africa’s president, Cyril Ramaphosa, and Kagame announced after a bilateral meeting in Kigali that they were determined to normalise ties.

Relations had been soured by Pretoria’s expulsion of three Rwandan diplomats suspected of involvement in the shooting in 2010 of Kayumba Nyamwasa, Rwanda’s former army chief of staff and a co-founder of Karegeya’s opposition party.

Mathopa gave South African police 14 days to detail what steps, if any, had been taken to arrest the four suspects in the Karegeya case, “since their whereabouts and their identity are known”.

His instructions theoretically pave the way either for a formal extradition request to be lodged with Kigali by the South African authorities or for international arrest warrants to be issued.

Asked about Monday’s developments, Rwanda’s high commissioner to South Africa, Vincent Karega, said: “I am not party to discussions in the inquest to know what is being discussed.”

Monday’s ruling marks a triumph for the South African activist group AfriForum and the head of its private prosecutions unit, Gerrie Nel, who last week called for the inquest to be suspended, warning of a cover-up. The Karegeya family approached AfriForum for help after becoming frustrated at the years of judicial inaction.

Members of the Karegeya family, gathered in the Randburg court, welcomed the development, saying they had always wanted a prosecution brought and international arrest warrants issued, rather than an inquest.

“We are overjoyed,” said David Batenga, Karegeya’s nephew. “We never asked for an inquest, we were just presented with one. We needed prosecution, we needed our day in court, we needed justice. This case is finally getting the attention it deserves.”

Leah Karegeya, the victim’s widow, flew over from the US, where she has been granted political asylum, to give evidence. “The link between the suspects and the Rwandan government is very clear,” she said. “We have always known that, but it’s good to hear it said in court.”