The skeletal remains, along with personal equipment such as binoculars, military food rations and weapons, were uncovered in September in a cave on the island of Wakde in Papua province.
Researchers believe the cave may have contained hundreds of sets of remains, Indonesia's Antara state news agency said.
Koshin Kiyohara, an attache at the Japanese Embassy in Jakarta, said the mission had no information about the find. He said Japanese diplomats were still trying to verify the Antara report.
New Guinea, the western half of which is now the Indonesian province of Papua, was the scene of fierce combat between Japanese and Allied forces starting in 1942.
The Japanese heavily fortified Wakde with more than 100 bunkers, as well as 12 fortified coral caves. It also contained an airstrip that covered almost half of the island.
The Allies launched a massive aerial and amphibious assault on the tiny island on May 17, 1944. Allied reports say 40 Americans were killed in the operation, along with 759 Japanese soldiers, reports the AP. I.L.