By David McKenzie, CNN

Johannesburg (CNN) — The most wanted fugitive accused of involvement in the Rwandan genocide of 1994 has been arrested in Paarl, South Africa after decades on the run, authorities say.

Fulgence Kayishema was captured Wednesday in a joint operation between South African authorities and a UN team charged with finding the remaining fugitives, according to a statement.

When he was arrested in the late afternoon, Kayishema initially denied his identity, investigators said. But by the end of the evening he told them: “I have been waiting a long time to be arrested.”

Investigators said he used multiple identities and forged documents to evade detection.

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

“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 United Nations’ 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,” Brammertz said.

Huge reward offered

In recent years, the IRMCT prosecutor has complained about the lack of cooperation from South African authorities and there have been a series of near misses capturing Kayishema. But on Thursday, Brammertz lauded the cooperation and support of the South African government.

The events in Nyanga, Rwanda, were one of the most brutal of the genocide, in which an estimated 800,000 Tutsis and moderate Hutus were killed over the period of 90 days.

The tribunal alleges that Kayishema directly participated in the “planning and execution of this massacre.” The indictment says he bought and distributed petrol to burn down the church while refugees were inside. Kayishema and others are also accused of using a bulldozer to collapse the church following the fire, while refugees were still inside.

The office of the IRMCT says the investigation spanned multiple countries across Africa and in other regions.

A reward of up to $5,000,000 was offered by the US War Crimes Rewards Program for information on Kayishema and the other fugitives wanted for perpetrating the Rwandan genocide.

Kayishema is due to be arraigned on Friday in a Cape Town court.

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

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

The-CNN-Wire