Munyakazi, a linguistics professor who taught French in Baltimore until suspended in 2008, was flown back to Kigali Wednesday and handed over by US officials to face multiple charges after he had lost appeals to avoid extradition.
Rwanda's prosecutor general, Richard Muhumuza, said the professor was considered one of the genocide's key ideologues.
The charges, including crimes against humanity, relate to Munyakazi's actions in the former prefecture of Gitarama, said Faustin Nkusi of the prosecutor's office.
On April 19, 1994, during a speech, Munyakazi allegedly urged Hutus to kill Tutsis.
The indictment said he also shot and killed a resident in the southern village of Kirwa, and participated at roadblocks where Tutsis were identified to be killed.
More than 800,000 ethnic Tutsis and moderate Hutus were killed by Hutu extremists during a three-month rampage.
Munyakazi fled Rwanda in 2004 while awaiting trial on bail and taught French, reportedly in Baltimore and Alabama, while still maintaining his innocence.
"This is the fourth deportation from the United States, where have sent 21 arrest warrants for genocide suspects, said prosecutions spokesman Nkusi.
Officials already convicted
In December last year, the Tanzanian-based International Criminal Tribunal for Rwanda was closed after convicting 61 people of involvement in the genocide, including former leading military and government officials.
In early July this year, a French court sentence two Rwandan mayors, Tito Barahira and Octavien Ngenzi, to life in prison over the massacre of some 2,000 Tutsis on April 13, 1994 in the eastern Rwandan town of Kabarondo.
Those killed had sought refuge in a church.
Lawyers for both have since said they will appeal their verdicts as has the former head of the Rwandan intelligence service, Pascal Simbikangwa.
In 2014, he was convicted in the first such trial in France of genocide and complicity of crimes against humanity and sentenced to 25 years in prison.
(DW)