Military spokesperson, Colonel Mohammed Aidi, told Antara News that an officer was killed on Friday in Puncak Jaya regency.
Mr Aidi said members of a criminal group were responsible, a likely reference to the West Papua Liberation Army, which is operating in the area.
It comes amid a joint police and military operation in the Highlands to hunt Liberation Army members responsible for violent attacks late last year.
Mr Aidi said a group of Defence Force soldiers were carrying out “logistics distribution” in Puncak Jaya on Friday, when they were attacked.
The joint operations in the central Highlands, which extend to the regencies of Nduga, Puncak, Puncak Jaya and Lanny Jaya, are a response to the killings of at least 16 Indonesian road construction workers and a soldier in early December, which the Liberation Army has claimed responsibility for.
The armed group accused the workers of being Indonesian military spies, a claim rejected by the military.
Last week, Mr Aidi told RNZ Pacific one “separatist” had been killed this year during operations in Nduga.