National Capital District Governor Powes Parkop is renewing his call on the government to review its position on West Papua.
He wants it to support a legally supervised referendum for local Papuans to decide to remain part of Indonesia or become an independent state.
His call comes amid the escalation of conflict 10 days ago in Papua province, which was sparked off by the jungle-camp killing of 16 labourers the West Papua National Liberation Army said were soldiers.
"Only a properly supervised and legally conducted referendum in accordance with international law will solve this crisis or issue," he said. "Any other decision or approach will only prolong the problem and suffering of the Papuan people."
The former Dutch colony, rich in natural resources, declared itself independent in 1961, but Indonesia assumed its control in 1963 on the condition that it was to conduct a referendum. It was annexed six years later through a United Nations-backed vote that was seen as fraudulent.
"The campaign for self-determination won't stop," Parkop said. "Indonesia will never win the war of hearts and mind. They might win some battles, but will lose the war.
"The spirit of independence will never die because the vote in 1969 was never conducted on the basis of universal suffrage and in accordance with the law. As long as Indonesia does not do anything about that the flames of independence, it will escalate beyond their control. The only solution is proper, legally-held referendum."