Rear Adm Iskandar Sitompul said assailants armed with guns and machetes ambushed an army vehicle, killing three sergeants, one private and two civilians.
Earlier in the day, another attack on an army post in the same area killed an army private and wounded a lieutenant, Sitompul said.
He believed the same group of more than 20 gunmen was responsible for both attacks in Tinggi Nambut, a village in the mountainous district of Puncak Jaya.
"They are believed to be old players who always try to disturb the situation there," Sitompul said.
The former Dutch colony of Papua was incorporated into Indonesia in 1969. The poorly armed Free Papua Movement has battled for independence since then.
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