South Africa’s judicial system is trying to cover up the murder of former Rwandan intelligence chief Patrick Karegeya, a high-profile lawyer has told a magistrates’ court in Johannesburg, calling for a planned inquest to be replaced by proper investigation and prosecution of the perpetrators.

In an application filed after the inquest opened in the north-west suburbs of Johannesburg, advocate Gerrie Nel alleged on Wednesday that the methods used and identities of four Rwandans who killed Karegeya had been known “to everyone” for five years, yet no serious attempt had been made by the South African authorities to secure their arrest.

Karegeya, a former aide to President Paul Kagame who set up an opposition party in exile, was strangled on New Year’s Eve in 2013. He’d been invited to the five-star Michelangelo hotel in the Sandton district by a visiting Rwandan businessman friend and was found the following day.

His family and members of the Rwanda National Congress (RNC) claim the former head of external intelligence was the victim of a hit squad operating on Kagame’s orders. They have been pressing for those responsible to be brought to justice ever since. As the years have passed, some voiced fears the case was simply too sensitive to ever be pursued to its end.

Patrick Karegeya’s wife, Leah, in court on Wednesday. Photograph: Jhua-nine Wyrley-Birch/Michela Wrong

Nel, who represents AfriForum – a South African NGO campaigning on behalf of minorities, asked magistrate Jeremiah Matopa to halt the inquest and for a semi-completed investigation to be finalised. “We submit that this is an abuse of process,” he said. “This is a cover-up to disguise an inability to, and/or prohibition to, deal with an assassination.”

The inquest, the date of which was announced last November, raises concerns about Kagame’s standing as a respected international statesman and brings unwanted attention to the feted leader.

While Rwanda enjoys a reputation as a “donor darling”, with western development officials and philanthropic foundations marvelling at the country’s progress on key indicators since the 1994 genocide, human rights groups allege that it is a regime ruled by an iron fist.

Karegeya’s death was the most prominent in a series of murders, kidnappings, renditions and harassment suffered by Rwandan opposition members, social activists and journalists both inside the country and in exile over the last two decades.

Nel’s application, which was both read out in court and entered as evidence in the case, identifies the four alleged Rwandan perpetrators as “Appollo Ismael Kiririsi” (sic), “Alex Sugira”, “Samuel Niyoyita” and “Nshizrungu Vianney”.

“Inexplicably,” said Nel, “there was no indication that any steps were taken to trace the suspects.” No extradition requests had been made, either, he added. “There was no contact with Interpol or any other international law enforcement agency.”

The magistrate adjourned proceedings and said he would rule on the application on Monday morning.

South Africa’s National Prosecuting Authority issued instructions on 5 June 2018 for no prosecution to be brought, which raises further questions of political interference.

That was just three months after South African president Cyril Ramaphosa and Paul Kagame publicly announced their determination at a meeting in Kigali to normalise relations.

The relationship between the two countries has been strained since March 2014, when South Africa expelled three Rwandan diplomats in the wake of one of a total of four attempts on the life of Kayumba Nyamwasa, Rwanda’s former army chief of staff and a co-founder of Karegeya’s RNC. Kayumba lives under 24-hour armed guard in South Africa because of concerns about his security.

When asked if he believed there had been top-level political meddling in the case, Nel told journalists: “I’m just making an inference, based on all the evidence that was collected.”

But Karegeya’s widow, Leah, who lives in the US and flew in to Johannesburg for the inquest, believes otherwise. “The government which did this is still meddling,” she claimed to journalists at the end of the hearing. “The government of Rwanda is still delaying this.”

Nel, a former public prosecutor, is a high-profile figure in South Africa. He was chief prosecutor in the trial of the sprinter Oscar Pistorius for the shooting of his girlfriend Reeva Steenkamp in 2014, but later left government service to work at AfriForum, where he is representing members of the Rwandan diaspora in Johannesburg.