Wenceslas Twagirayezu, who works in IT, was flown back to Rwanda on Tuesday evening after losing an appeal against extradition earlier this year.
During the 1994 genocide, some 800,000 people, mainly minority Tutsis, were slaughtered by the military and by Hutu militias.
At the time, Twagirayezu was a teacher at a primary school in northern Rwanda but was also the local representative of the CDR (Coalition for the Defence of the Republic), an extremist Hutu movement, Kigali prosecutors say.
Twagirayezu, who was born in 1967, fled Rwanda in 1997 and arrived in Denmark in 2001. He was granted residency in 2002 and became a Danish citizen in 2004.
“Twagirayezu is accused of genocide, extermination and murder as crimes against humanity,” the Rwandan prosecutor's office said, referring to his alleged role in attacks against Tutsis in the areas around Gisenyi, a city on the northern tip of Lake Kivu.
“He participated in the mass killing and extermination of Tutsi.”
According to the indictment, one of the attacks which Twagirayezu was involved in targeted a parish church in Bususamana where at least a third of the 3,000 Tutsis who were taking refugee there were killed.
The prosecution said Twagirayezu would face a “fair trial” and called on other countries where “Rwandan genocide fugitives are still moving freely” to take the appropriate action to bring them to justice.
His extradition came as prosecutors in Belgium said they would put five Rwandans on trial over their role in the 1994 genocide.
Twagirayezu is the second suspect to be extradited from Denmark on suspicion of involvement in genocide after Emmanuel Mbarushimana was handed over to the Rwandan authorities in 2014.