Craig Skehan Kupang and Greg Roberts Brisbane – Aid and church groups are concerned that thousands of East Timorese refugees in camps in West Timor could be used as bargaining chips in Indonesia's stand-off with the international community.

These concerns have been heightened by the refusal of authorities to allow independent monitoring of the camps and reports that thousands of East Timorese are being forcibly driven across the border by the Indonesian military.

Indonesian soldiers, police and anti-independence militia are tightly controlling access to refugee camps and are imposing tough restrictions on the foreign media. Indonesian authorities argue that the refugees are opponents of independence.

UN officials in the West Timorese capital Kupang today estimated that at least 68,000 East Timorese refugees had come across the border while Catholic Church sources in the West Timorese town of Atambua say up to 100,000 refugees have been crowded into just four camps.

The Catholic Church is worried about the safety of the refugees after the reported murder of two pro-independence East Timorese men in Atambua yesterday by militia members. A church official said the men were singled out and shot in front of dozens of other refugees.

Church sources in Atambua and Kupang said militia members had a strong presence in West Timorese territory along the road between Atambua and the border, an 80-minute drive, and were stopping vehicles heading west.

Although it is not possible to confirm the figures, sources in Atambua said more than 40,000 refugees had arrived by yesterday afternoon. Many are staying in church buildings. Some have been taken in by West Timorese families. Others are camped in the open.

In the town of Kepa, 25,000 refugees have arrived. There are about 20,000 in the village of Soa and another 20,000 in Betun. An unknown number are in Kupang and other West Timorese centres, with Amnesty International claiming 8000 are in the town of Kefamenanu.

In Atambua, Catholic workers have asked the Indonesian Government for medical supplies to cope with the refugee flow, and water is in short supply in some places.

With most refugees doing their best to stay away from Government-run camps in West Timor, the province's two bishops – Bishop Petrus Turang of Kupang and Bishop Antonius Tain Ratu of Atambua – have opened the doors of church property to the East Timorese.

The leading contender to become President of Indonesia, Mrs Megawati Sukarnoputri, arrived in Kupang, where she was enthusiastically greeted by the Governor of East Timor, Abilio Soares, a strong opponent of independence.

He said the Indonesian Parliament could refuse to ratify East Timor's vote for independence.

Indonesian journalists were allowed to film and photograph Mrs Megawati. Mrs Megawati's staff warned foreign journalists not to follow a convoy to refugee camps on the outskirts of Kupang because it would be "too dangerous".