According to a charge sheet seen by Reuters, Kayishema faces five charges in South Africa, including two of fraud.
The fraud counts relate to applications he made for asylum and refugee status in South Africa, where the National Prosecuting Authority (NPA) alleges he gave his citizenship as Burundian and used a false name.
Kayishema was not asked to enter a plea at Cape Town Magistrates' Court, which adjourned the matter to June 2.
As he was being brought up from the dock, Kayishema was asked by a journalist if he had anything to say to the victims of the 1994 genocide, to which he responded: "What I can say? We are sorry to hear what was happening".
"It was a war at that time... I didn't have any role," he added.
On the run for two decades, Kayishema was arrested on Wednesday under a false name on a grape farm in Paarl, 59km from Cape Town.
He was a fugitive from justice since 2001 when the International Criminal Tribunal for Rwanda indicted him for genocide over his alleged role in the destruction of the Nyange Catholic Church in Kibuye Prefecture.
An estimated 800,000 ethnic Tutsis and Hutu moderates were killed during Rwanda's genocide, orchestrated by an extremist Hutu regime and meticulously executed by local officials and ordinary citizens in the rigidly hierarchical society.
Kayishema has been on the US State Department's wanted list under the Rewards for Justice Programme, with a $US5 million ($A7.7 million) reward offered for his arrest.
Kayishema had legal representation in court on Friday and agreed to have proceedings in English without a translator.
There was a heavy police presence in court, with masked police officers carrying automatic weapons and bullet-proof vests.
Kayishema was wearing a blue rain jacket, black trousers and black leather boots.Â
He was clean-shaven and carried a Bible and a blue book of dedications which had "Jesus First" emblazoned on its cover.
Kayishema will be held at Cape Town's Pollsmoor Prison ahead of his possible extradition to Rwanda.
