Suharto, who led a regime widely regarded as one of the 20th century's most brutal and corrupt, has lived a reclusive life in a comfortable villa in downtown Jakarta for the past decade.
He had been in and out of the hospital several times since being toppled by a pro-democracy uprising during the 1997-1998 Asian financial crisis for heart problems and internal bleeding.
Historians say up to 800,000 alleged communist sympathisers were killed during Suharto's rise to power from 1965 to 1968. His troops killed another 300,000 in military operations against independence movements in Papua, Aceh and East Timor.
Suharto's poor health has kept him from facing trial, and no one has been punished for the killings.