Brigadier General Gusti Putu Danny, the head of Papua's Intelligence Agency was shot near Dambet Village in the Puncak District on Sunday.
The Indonesia's president has ordered a crackdown on what he calls armed criminal groups.
The Indonesian media has also reported the chairman of the People's Consultative Assembly in Papua, Bambang Soesatyo, urging the government to deploy forces at full strength to crush the Papuan rebellion.
He is quoted saying "destroy them first. We will discuss human rights matters later."