He was 93.
Kabuga was arrested in France in 2020 after more than two decades on the run and extradited to The Hague.
He was ruled unfit to stand trial in 2023 because of dementia and was also deemed too ill to return to Rwanda.
With no country willing to accept him, Kabuga remained in the UN detention centre in The Hague.
The court said it had ordered an inquiry into the circumstances of his death.
Kabuga died while hospitalised in The Hague, the court said.
The former businessman and radio station owner was among the last fugitives sought over the genocide, in which Hutu extremists killed more than 800,000 Tutsis and moderate Hutus in 100 days.
Prosecutors accused Kabuga of promoting hate speech through his broadcaster Radio Television Libre des Mille Collines and of helping arm ethnic Hutu militias.
The court that announced his death, the Mechanism for International Criminal Tribunals, oversees remaining cases from the former UN tribunals for Rwanda and the former Yugoslavia.
The Rwanda genocide was triggered on April 6, 1994, when a plane carrying then-president Juvénal Habyarimana was shot down and crashed in the capital Kigali, killing the leader who - like the majority of Rwandans - was an ethnic Hutu.
Kabuga's daughter married Habyarimana's son.
with AP
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