The question to be asked about the bloody ambush in the Indonesian province of Papua of employees of the giant US-owned Freeport mine is who stands to gain. The Indonesian military has been quick to blame separatist guerillas.

However, on the face of it, the weekend ambush which killed two American teachers, an Indonesian mine worker and wounded 11 others could only discredit the Papuan independence movement. At the same time, the murders are expected to provoke a security crackdown in the remote province where indigenous tribal people have resented and resisted Jakarta's authority since their incorporation into Indonesia more than three decades ago.

It is plausible that a hardline, armed Papuan faction posted the gunmen along the isolated road. However, at no time in the past have Papuan fighters targeted foreigners. The ambush occurred just as local military commanders embarked on a 60-day campaign to shut down the political wing of the Papuan independence movement. Indonesia's military is seeking a resumption of military ties – and funding – from the United States. As such, it is keen to co-operate in protecting US interests overseas. The Freeport operation is the world's biggest copper and gold mine.

Papuan leaders blame the Indonesian military for the ambush, calling it a "set-up" to justify a new round of arrests. That such a conspiracy should even be entertained is a measure of the Indonesian military's poor record of unprofessional, politicised conduct. Twelve members of the notorious Special Forces unit were charged with the murder last year of the West Papuan leader, Theys Eluay, a widely respected moderate who was seeking a negotiated peace settlement. Such a peace would have allowed the demilitarisation of the resource-rich province, disadvantaging senior military commanders who have built their careers and personal fortunes on the back of the protracted conflict.

After East Timor, the Indonesian Government is determined to combat separatism in Papua and the northern province of Aceh. But this can be achieved only through an end to human rights abuses and the return of a fairer share of the province's wealth to the indigenous people. The implementation of a recent autonomy package has been slow and uneven. The Freeport murders must be independently investigated and not used to justify further repression. Such independent action is necessary to ensure all suspects are properly scrutinised, even the military itself.