The former Rwandan army colonel, Dioniste Pagosora, has been accused of being the mastermind of a genocide in his country that killed 800,000 people in 1994.
Pagosora, 80, was serving a prison sentence in Mali.
In the first phase, the International Criminal Court for Rwanda sentenced Pokosora to life imprisonment, but reduced the sentence to 35 years.
His father Achilles told the BBC his father died at Bamako Hospital, where he was being treated for heart problems.
In the 100 days since the genocide, 800,000 people, mostly Tutsis, have died.
The assassination began on April 6, 1994, when a plane carrying then-Rwandan President Juvenile Hapiermanna was shot down, killing all on board.
Pokosora was arrested two years later in Cameroon, where he fled after Paul Kagame-led Rwandan Patriotic Front seized power in the country.
He was indicted by the International Criminal Court in 2008 for crimes against humanity and the assassination of several political figures, including Prime Minister Agatha Olengimana.
Pokosora insisted at trial that he was the victim of a campaign by the current Tutsi-dominated Rwandan government.
Canadian Army Major General Romeo Taller, who commanded UN peacekeepers during the genocide, described Pokosora as the “brain” of the killings. He added that the former colonel had threatened to kill himself.
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