The Residual Special Court for Sierra Leone said an enquiry would be opened after Alex Tamba Brima, 44, died at King Faisal hospital in Kigali following a "serious illness".
As a leader of the Armed Forces Revolutionary Council (AFRC), Brima helped to depose president Ahmad Tejan Kabbah in May 1997, before setting up one of the most vicious juntas Africa has ever known.
A supporter of former Liberian president Charles Taylor, Brima was tried with two others on war crimes charges ranging from murder, mutilations of civilians, rape and enlisting child soldiers.
Momoh Sillah, a former cocoa plantation farmer and double amputee as a result of long war, told AFP by phone the rebel commander had paid for his actions.
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"Speak no evil of the dead, they say, but for all I care, Tamba can go and rot. He has finally paid for his deeds," he said.
Sillah said rebels loyal to the AFRC leader caught him at his plantation in 1999 as they rampaged through the countryside.
When he was first convicted in 2007, judge Julia Sebutinde said Brima and his co-defendants were guilty of some of the "most heinous, brutal and atrocious crimes" humanity had ever known.
He was sent to Rwanda with seven others under a special arrangement in 2008 as it was deemed Sierra Leone did not have proper facilities for their detention.
Three years later his family alleged that since his arrival in Kigali in October 2009 he had suffered poor nourishment and a lack of access to medical facilities.
"We have not been told whether the body will be released to us or not," the source added.
The Special Court for Sierra Leone was established by the UN in 2002 to try those who bore "the greatest responsibility" for the atrocities during the civil war, and was succeeded by the residual court in 2013.