Eight separatists were killed and several injured after troops raided a camp in the Wamena region on Wednesday morning, an army officer told El-Shinta radio.
"We launched the raid at 5am and confiscated weapons from them... It is suspected that they had been planning to carry out attacks on a regency office and local military headquarters," Colonel Agus Mulyadi said.
Security forces were not available for immediate comment.
In a separate incident, four people were killed and four others including a policeman were wounded after an armed group attacked a security post in the remote town of Enarotali on Tuesday.
The official news agency Antara, said those killed were civilians.
Resource-rich Papua, on the eastern end of the sprawling archipelago, is one of Indonesia's separatist hotspots where clashes between security forces and rebels break out
The Free Papua Movement has been waging armed resistance against Jakarta since Papua's forced incorporation into Indonesia in 1963.
A UN-run referendum in 1969 held among leaders of the local population resulted in a decision to join Indonesia, but the vote has been widely criticised as unfair.