The chairman of the Papua and Aceh special autonomy supervisory team, Priyo Budi Santoso, urged the government to send the military to Papua if the referendum movement escalated to a mass rebellion.
Thousands of Papuans across the province have demonstrated to call for a referendum on independence.
The demonstrations coincided with a series of attacks on police and military posts in Puncak Jaya that have been blamed on the Free Papua Movement (OPM).
"I urge law enforcers not to hesitate in taking firm action," he said.
He added that if the situation escalated to rebellion, the "military should be sent in if necessary".
"We should remain persuasive but if the situation leads to [demands for] a referendum; [we] should not hesitate in sending in the military," he said, adding that special autonomy was the "best formula in addressing the problems of Papua".
"Therefore, I urge the government to firmly reject [the calls for a referendum] because Papua is part of Indonesia and that is final," he added.