Kayishema appeared briefly in a Cape Town court before his case was postponed to June 2.
The former Rwandan police officer, 62, was arrested on Wednesday in Paarl, a town in South Africa’s Western Cape Province, after being on the run for 22 years.
He is accused of orchestrating the killing of approximately 2,000 Tutsi refugees at the Nyange Catholic Church during the 1994 genocide against the Tutsi in Rwanda.
An estimated 800,000 Tutsis and moderate Hutus were killed in Rwanda in 1994 during a 100-day bloodshed.
Kayishema was arrested in a joint operation by South African authorities and fugitive tracking team of the International Residual Mechanism for Criminal Tribunals (IRMCT), according to a statement released by the special UN tribunal on Thursday.
IRMCT chief prosecutor Serge Brammertz said Kayishema was a fugitive for more than 20 years and “his arrest ensures that he will finally face justice for his alleged crimes.”
The IRMCT said genocide is the most serious crime known to humankind and the international community has committed to ensuring 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,” the statement said.
The UN on Thursday welcomed the arrest of Kayishema, saying: "Mr. Kayishema’s apprehension sends a powerful message that those who are alleged to have committed such crimes cannot evade justice and will eventually be held accountable, even more than a quarter of a century later," Stephane Dujarric, the spokesman for UN Secretary-General Antonio Guterres, said in a statement.