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Their report estimates that 400,000 to 500,000 people -- believed associated with the communist party, were killed by military deaths squads, but indicates that official secrecy around these numbers makes the actual figure hard to gauge.
The panel, presided over by head judge Zak Yacoob, a former South African Constitutional Court Justice, held a four-day hearing in the Hague in November of last year, where they heard over 20 witnesses, some of whom gave evidence behind a screen to protect their identity.
In their damning report issued Wednesday, the judges listed a number of allegations which they found to be well founded; including inhumane, ruthless torture, unjustifiable imprisonment and "forced labor that might well have amounted to enslavement."
The panel also found evidence of systematic sexual violence, political persecution and exile, and disappearances of thousands who were thought not to support the Suharto dictatorship with "sufficient fervor."
The judges recommended the Indonesian government apologize to victims and their families, investigate the crimes against humanity, and ensure any survivors receive appropriate compensation.
However, Coordinating Political, Legal and Security Affairs Minister Luhut Pandjaitan told press Wednesday that Indonesia had its own legal system, that no external party could dictate the way it solved its problems and that the government would not bow to the IPT 1965's recommendations.
"Our country is a great nation. We acknowledge and we will resolve this problem [the 1965 tragedy] in our way and through universal values," Luhut said at the Presidential Palace on Wednesday.
Complicity and a failed coup
The report also states that the United States of America, the United Kingdom and Australia were fully aware of what was taking place in Indonesia and were complicit to varying degrees.
The report says the three countries were invited to take part in the investigation, but did not accept the invitation. None of the countries have responded to the findings.
The 1965 bloodbath was sparked by a failed coup and the murder of a number of generals in the military. A major general in the army at the time, Suharto blamed the coup on communists, ousted President Sukarno -- the country's first post-independence leader -- and sanctioned a hunt for those responsible.
After assuming the presidency in 1967, Suharto ruled Indonesia for 31 years until 1998.
Human rights groups have previously estimated that as many as 1 million people may have been killed by military death squads, and many contend that those targeted during the purges were not communists but ethnic Chinese, or anyone with left wing views.
The Foundation IPT 1965 (International People's Tribunal) was formally established in 2014 and consists of Indonesian exiles, human rights activists, members of victims' organizations and researchers.
They organized the International People's Tribunal on the 1965 Crimes Against Humanity in Indonesia in response to an "absence of an official domestic process of transitional justice based on truth finding," according to a statement.