The cause of the crash that killed a dozen soldiers on board the Russian-made Mi-17 remains under investigation.
The soldiers' remains were retrieved on Saturday, after villagers found the wreckage last week.
Sebby Sambom, a spokesman for the West Papua National Liberation Army, the military wing of the Free Papua Movement, told The Associated Press that they had located the wreckage in September and managed to seize weapons and ammunition in December.
"It has become our target and natural forces had helped us to take it down," Sambom said, "Their weapons are a treasure trove of our struggle."
Photos sent by Sambom from the wreckage site showed several assault rifles, pistols, magazines and a large cache of ammunition next to a flag of the West Papua's independence movement, the Morning Star.
Papua military chief Maj Gen Herman Asaribab acknowledged that 11 weapons -seven SS-1 assault rifles, three pistols and a grenade launcher - had been stolen from the crash site.
But he denied the rebels claim, saying the weapons might have been taken by hunters and "we will approach them to return all the 11 weapons immediately."
The helicopter lost contact five minutes after takeoff from Oksibil, the capital of the district of Bintang Mountain on June 28. It was traveling to the provincial capital, Jayapura.
The helicopter was taking troops and supplies to a border post in Okbibab near Papua New Guinea and had refueled at Oksibil before it was reported missing by the control tower, the military said.
Flying is the only practical way of accessing many areas in the mountain and jungle-clad easternmost provinces of Papua and West Papua where an insurgency has simmered since the early 1960s, when Indonesia annexed the region that was a former Dutch colony.
Papua was formally incorporated into Indonesia in 1969 after a UN-sponsored ballot that was seen as a sham by many. - AP