Kayishema was directly involved in the "planning and execution" of the massacre of more than 2,000 Tutsi refugees in Nyanga Catholic Church during the Rwandan genocide.

The most wanted fugitive accused of involvement in the 1994 Rwandan genocide was arrested Wednesday in Paarl, South Africa, after decades on the run, authorities said.

Fulgence Kayishema was arrested in a joint operation involving South African authorities and the prosecutor's fugitive-tracking team, said the chief prosecutor of the tribunal charged with finding the remaining fugitives.

Kayishema, who has been on the run since 2001, allegedly orchestrated the killing of more than 2,000 Tutsi refugees -- women, men, children, and the elderly -- at Nyange Catholic Church in Rwanda during the genocide.

"Fulgence Kayishema was a fugitive for more than 20 years. His arrest ensures that he will finally face justice for his alleged crimes," said Chief Prosecutor Serge Brammertz of the International Residual Mechanism for Criminal Tribunals (IRMCT).

"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," he added.

Brammertz has complained in recent years about the lack of cooperation from South African authorities, and there have been a series of near misses capturing Kayishema. On Thursday, however, he hailed the cooperation and support of the South African government in apprehending the fugitive.

The events in Nyanga were one of the most brutal of the genocide that saw an estimated 800,000 Tutsis and moderate Hutus killed over the period of 100 days.

The tribunal alleges that Kayishema, who is due to appear in a Cape Town court Friday, was directly involved in the "planning and execution of this massacre".

According to the indictment, he bought and distributed petrol to burn down the church while refugees were inside. Alongside others, Kayishema is also accused of using a bulldozer to demolish the church after the fire, while refugees were still inside. 

The IRMCT says the investigation leading to his arrest spanned multiple countries across Africa and in other regions. The US War Crimes Rewards Program offered a reward of up to $5,000,000 for information on Kayishema and the other fugitives wanted for perpetrating the Rwandan genocide.

The Rwandan genocide saw Hutu militias and civilians alike kill large numbers of members of the Tutsi ethnic minority: men, women and children, many of whom had been their neighbours before the genocide began.

The killings finally ended 100 days later, when Rwandan Patriotic Front (RPF) troops, led by Paul Kagame, defeated the Hutu rebels and took control of the country.