One of the world’s most wanted genocide suspects, a Rwandan former police chief, Fulgence Kayishema, has been arrested in South Africa and charged with playing a leading role in the murder of more than 2,000 people in a church in April 1994.

Kayishema has spent more than two decades as a fugitive and was living under a false name at the time of his arrest on Wednesday afternoon in Paarl, 35 miles (60km) north-east of Cape Town. He was detained by the South African police and members of a tracking team from the Rwandan war crimes tribunal based in Arusha, Tanzania.

Serge Brammertz, the tribunal’s chief prosecutor who led the hunt, said: “Fulgence Kayishema was a fugitive for more than 20 years. His arrest ensures that he will finally face justice for his alleged crimes.

“Genocide is the most serious crime known to humankind. The international community has committed to ensure that its perpetrators will be prosecuted and punished. This arrest is a tangible demonstration that this commitment does not fade, and that justice will be done, no matter how long it takes.”

Kayishema, 62, was one of four suspects indicted by the tribunal who were still not accounted for, from a total of 96 indicted, and he was possibly the last major suspect still living and at large. The tribunal only indicted the leading perpetrators; there are still more than 1,000 others wanted by Rwandan prosecutors for their alleged roles in the genocide, in which more than half a million people were killed in 100 days.

Brammertz paid tribute to the South African authorities for their assistance.

“The thorough investigation that led to this arrest was made possible through the support and cooperation of the Republic of South Africa and the operational task team established by President [Cyril] Ramaphosa to assist our fugitive tracking team,” he said. “Their exceptional skills, rigour and cooperation were critical for this success.”

Brammertz serves as prosecutor for the residual mechanism set up in 2010 to deal with outstanding cases from international criminal tribunals for Rwanda and the former Yugoslavia. All 161 indicted suspects from the former Yugoslavia have been accounted for.

At the time of the genocide in 1994, Kayishema was a Hutu police inspector in Rwanda’s Kivumu commune, in the north of the country. He is accused of playing a leading role in rounding up Tutsis in the area and confining them in the compound of a parish church in the settlement of Nyange, where some Tutsis had already sought refuge.

The church was surrounded by Kayishema’s police and members of the Hutu Interahamwe militia who launched an attack on the thousands of civilians inside on 13 April 1994, hacking at them with machetes and throwing grenades into the crowd.

The survivors, many of them women, children and the elderly, barricaded themselves in the church as the siege went on for three days. A bulldozer was brought in to demolish the church, bringing its roof down on the people inside. Anyone found alive in the ruins was killed.

A statement from Brammertz’s office said: “The investigation leading to Kayishema’s arrest spanned multiple countries across Africa and elsewhere. During his flight from justice, Kayishema utilised many aliases and false documents to conceal his identity and presence.”

Among those already convicted for the church massacre is the parish priest Athanase Seromba, who was convicted of organising the killings alongside Kayishema. He had hidden in Italy with the help of the Catholic church but surrendered in 2002. The international criminal tribunal for Rwanda (ICTR) sentenced him in 2006 to 15 years in prison, which was increased to a life sentence on appeal in 2008.

Just over a year ago, Brammertz’s tracking team found the body of another major genocide suspect, Protais Mpiranya, the former head of the presidential guard, buried under a false name in Zimbabwe, where he had been living as a fugitive.