Indonesia's military, or TNI, says its soldiers have taken control of an regional headquarters of the West Papua Liberation Army in Papua's Highlands.
Armed conflict between the Liberation Army and the TNI since late last year has left dozens dead in Nduga regency.
Thousands of villagers have also been displaced from the regency due to the conflict.
A TNI spokesman, Muhammad Aidi, said in recent days TNI forces succeeded in taking control of the Liberation Army headquarters in Mugi District of Nduga.
An array of weapons and ammunition was seized in the process.
Antara reported Colonel Aidi saying the security situation in the regency is increasingly conducive, although troops have been urged to remain alert for further attacks by the rebels.
The Liberation Army's guerilla fighters led by Egianus Kogoya shot and killed a TNI officer just over a week ago.