The bodies, in three graves inside the Indonesian province of West Timor, are believed to be from the town of Suai where some 100 people were shot and macheted trying to shelter from militias in the aftermath of August's vote for independence.
The graves were discovered by human rights investigators appointed by the government in Jakarta. "We found three bodies in the first grave, 11 in the second grave and 11 in the third grave," a member of the team, Munir, was quoted as saying in the Jakarta Post.
Three of the bodies have been identified as Roman Catholic priests last seen alive trying to shield some 2,400 people from the Laksaur (Eagle) militia. "We have performed autopsies on the bodies [of the priests]," Mr Munir said. "One died of gunshot wounds and the other two of knife wounds."
The fate of the Suai Catholics was one of the most agonising moments of the East Timor violence which erupted after the territory's population voted overwhelmingly for independence in the 30 August UN-supervised referendum.
On 4 September, the UN decided to evacuate Suai, to the dismay of the people, including Father Hilario, one of the most respected local priests.
"Father Hilario was beside himself when we left," a UN official said, a few hours after the evacuation. "He thinks they are all going to be massacred."