An international warrant was issued for his arrest and he is currently in police custody in Kigali, Rwanda’s capital, said the Rwanda Investigation Bureau.
Rusesabagina, 66, is accused of being the “founder, leader and sponsor of violent, armed, extremist terror outfits,” the agency said.
Rusesabagina gained prominence during the 1994 Rwandan genocide for saving the lives of hundreds people.
Around 800,000 Tutsis and moderate Hutus were killed in the genocide, which was led by Hutu extremists.
At the time, he was a manager at the Milles Collines hotel where he hid and sheltered people in the luxury hotel.
Rusesabagina has not lived in Rwanda since 1996 when he survived an assassination attempt.
He is the recipient of several human rights awards for his efforts during the genocide, including the US Presidential Medal of Freedom in 2005.