Reporter: Hamish Fitzsimmons

Peter Cave: A military build-up in the Indonesian province of Papua has heightened tensions between the Government and independence activists, and is said to have been prompted by the arrival in Australia last week of 43 Papuan asylum seekers.

There've been numerous reports of reprisal attacks, and local leaders say the military operations are intended to terrify the local population and quash separatist sentiments.

The Indonesian Government has also warned relations with Australia will be damaged if it accepts the Papuans as refugees.

Hamish Fitzsimmons reports.

Hamish Fitzsimmons: In recent weeks, the Indonesian military has been boosting its numbers in the province of Papua. It says it needs to bolster security, but local activists are wondering on what grounds.

The Reverend Socratez Sofyan Yoman is the Chairman of the West Papua Baptist Church. He says Indonesian tanks have been patrolling the streets of the provincial capital Jayapura and that the military build up is having its desired effect.

Socratez Sofyan Yoman: We are very, very afraid, very, very, very afraid, and the terrible situation in all Papuans in the provinces, also in the islands, in the coastal area. Because everywhere is military, now it's military base, everywhere they take their guns they go round and round. I think in West Papua now – right now – it's more military in here.

Hamish Fitzsimmons: After the 43 Papuan asylum seekers landed in Australia last week, there was an incident in the region many of them came from. At least one person was killed and others were wounded when the Indonesian military said it broke up a gang demanding illegal road tolls. But Sofyan Yoman claims it's part of a plan to terrorise the population.

Socratez Sofyan Yoman: They can't do that, terrorise the people, intimidate the people. For example, they kill the people in Waghete, they want to create a conflict like East Timor. They will justify, justify for the Indonesian military in West Papua, military operation in West Papua. We'll become... we'll be like East Timor.

Hamish Fitzsimmons: The Indonesian Government has warned that if Australia accepts the 43 Papuans as refugees, relations between the two countries could be damaged. The Federal Government maintains its respect for Indonesia's current sovereignty but Indonesian politics expert, Dr Richard Chauvel, says there's lingering suspicion of Australia after East Timor's independence in 1999.

Richard Chauvel: Australia as we'd all remember, supported Indonesian sovereignty and occupation of East Timor for decades, but in Indonesia eyes when the crunch came, that policy changed around very quickly.

They clearly recognised as the case was with refugees from East Timor that by granting asylum seeker refugee status to people the Indonesians regard as their citizens, that is by definition saying something about our views on human rights conditions within Indonesia.

Hamish Fitzsimmons: The Australian Government says it will assess the claims of the Papuans according to its legal obligations and the merits of their cases. The 43 people remain on Christmas Island awaiting news of their claims.

Peter Cave: Hamish Fitzsimmons reporting.