Now Indonesian human rights officials want Obama's help in addressing unanswered questions about the bloodshed 50 years ago. They are requesting the declassification of secret US files that could shed light on how the killings were planned and the extent that the United States collaborated with Indonesia's military.
Despite nearly two decades of civilian rule, the prevailing account in Indonesia of those events remains the one planted by the military regime that swept to power after the killings, led by the dictator Suharto who ruled for 30 years.
Joko Widodo, the first directly elected Indonesian president without links to Suharto, ran as a reformer who would look into episodes of military impunity, but since taking office in 2014, he has not pressed the issue due to opposition within his own government and the still-powerful military.
Indonesia's National Human Rights Commission in 2012 reported there was evidence that crimes against humanity were committed during the 1965-1966 crackdown, but the attorney general took no action.
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Commissioner Muhammad Nurkhoiron met this week with State Department officials and has made a formal request to Obama that says the release of files from the CIA, the Defense Intelligence Agency and other agencies will help in "encouraging the Indonesian government to redouble its own efforts to establish the truth" and promote reconciliation.
Myles Caggins, a National Security Council spokesman, said it will review the commission's request. He said the administration supports the declassification of any relevant documents from the period which do not pose a national security risk.
The US has already released many documents related to the period, but has withheld others.
The killings began in October 1965 shortly after an apparent abortive coup in which six right-wing generals were murdered.
In his 1995 best-selling memoir, "Dreams From My Father," Obama recounted how his mother, who had moved them to Jakarta after marrying an Indonesian, learned about the recent killings through "innuendo, half-whispered asides.