Some 16 new grave sites containing about 5,000 suspected victims of the Cold War killings were pinpointed on the country's main island Java, according to the organisation.
Historians say up to 500,000 alleged Indonesian Communist Party (PKI) supporters were killed between 1965-1966 by soldiers and civilian militias around the time General Suharto became president.
He blamed the Indonesian Communist Party for a failed coup and rose to power on the back of the bloodshed, going on to lead the world's most populous Muslim nation with an iron fist for three decades.
"One of the witnesses said his grandfather's job was to wash the dead bodies," said Bedjo Untung, head of the 1965 Victims Group.
Also Read
"He would follow his grandfather and saw him clean about 50 bodies a day," he added.
Untung -- who was imprisoned as a member of the Communist party in the mid 1960s -- urged Indonesia's human rights commission to investigate and protect the graves as well as members of his group.
A presidential spokesman did not immediately respond to a request for comment.
Last month, declassified US documents showed how American officials across the archipelago knew of the massacres, including the complicity of prominent Muslim civil society groups in the killings. But diplomats offered little public protest, keen to take advantage of the communist party's destruction at the height of the Cold War.
The 39 US embassy documents cover the period from 1964- 1968 and uncovered new details about one of the most tumultuous periods in modern Indonesian history.
But no concrete action to delve into the country dark's history or bring perpetrators to account has so far been taken.
Disclaimer: No Business Standard Journalist was involved in creation of this content