A human right organisation, Elsham, in the Indonesian province of Papua says the military killed ten people near Wamena last week because they had witnessed an armoury break in earlier this year.
The Indonesian military said last week the ten were killed because they were members of the militant Free Papua Movement, the OPM, and were planning an attack.
The local military commander, Colonel Agus Mulyadi, said the rebels had carried guns stolen from the armoury.
But an Elsham spokesman, Ronny Papilatu, says the ten were killed to stop them talking to Indonesia's national human rights committee which announced last week it would investigate events surrounding the break in.
The army had blamed the OPM for the break in but several soldiers have been implicated.
Meanwhile a spokesman for the OPM, John Ondawame, says last week's ambush was only possible because the Islamic militant group, Laskar Jihad, has recruited dozens of Papuans into pro-Jakarta militia.