The giant Freeport gold and copper mine is carving a scar so vast and deep into the remote forests of Papua that it will soon be visible from space. Downstream, a swelling bruise of a billion tonnes of mine waste has rendered wetlands inhospitable for aquatic life. The stupendous profits generated by the world's largest copper and gold mine largely pass the indigenous Papuans by. That the mine has become the violent flashpoint in their dogged campaign for independence is unsurprising.

Democracy in Indonesia has, rightly, raised expectations for accountability. The reckless polluters of Freeport, the abusive military units stationed in Papua and the civilian government in Jakarta are on notice: the bad old days of impunity are over.

Under the former authoritarian president Soeharto, foreign mining companies in Indonesia enjoyed cosy deals. The US-operated Freeport mine barricaded itself behind a security cordon and built an industrial city in the middle of one of the world's pristine, and most fragile, natural environments. A recent New York Times investigation revealed Freeport has made $US20 million in direct payment to Indonesia military officers – protection money to ensure Indonesian troops do the dirty work of keeping the ragtag Free Papua Organisation, with its spears and few rusty guns, away. Freeport employs 18,000 people and has pumped $US33 billion into the Indonesian treasury since 1992, contributing almost 2 per cent of gross domestic product. But like the oil and gas riches of Aceh, little wealth has been returned to the province, and local complaints are met with violence, intimidation and abuse.

Last week, thousands of angry Papuan demonstrators set upon and killed four Indonesian security officers. The murders, and the rage that sparked them, shocked many Indonesians. But as The Jakarta Post noted: "The reasons for the protests in Papua are obvious." If Papuans lose all hope for change the "situation could become more dangerous", it warned.

Australia does not support independence for Papua, but with 43 Papuan asylum seekers being processed, Canberra cannot ignore the new unrest.

There have been many empty promises of autonomy and demilitarisation for Papua since Soeharto's fall in 1998. Indonesia's military, with its vested interest, is undoubtedly frustrating change. The Bougainville copper mine in Papua New Guinea provides a warning. It provoked such a violent campaign for self-rule that it was abandoned in 1989. Almost a decade of conflict followed.

The glare of the international spotlight on Aceh following the tsunami forced a peace deal there. Papua deserves the same attention.