His music, once popular among the ruling elite, was swiftly banned.
Two years later he was accused of terrorism and raising support for an opposition political movement and sentenced to 10 years in prison.
His lawyers said prosecutors had little evidence to jail him. He was released on presidential pardon in September 2018.
Mihigo and Polly are not the first figures to die in mysterious circumstances while in police custody in Rwanda.
Last year, a former director-general in Kagame's office was found dead in a military jail after being sentenced to 10 years for corruption.
In 2015, Kagame's personal doctor, Emmanuel Gasakure, was shot dead in custody by police.
Kagame, who has been in power since 1994, has been accused of ruling with an iron fist, clamping down on all forms of dissent and jailing or exiling opposition politicians.
Human Rights Watch (HRW), among other groups, has accused Kagame's regime of summary executions, unlawful arrests and torture in custody.
Boutross: Mimi siwezi mind kuwekwa