Mark Dodd, Malibaka – It is only 8am but the sun is scorching, and the 23 East Timorese refugees squat in the shade at the Malibaka River checkpoint after crossing back into their homeland. Australian soldiers offer water and search their belongings for hidden weapons, but those returning are mostly old men, women and children. Nothing suspicious is found.

The refugees are glad to be back, but are nervous and unsure of the reception that awaits them. "I've come back because East Timor is my country – I used to live here," says Semedio Tovares. His clothes are grubby, and he wears a huge bronze crucifix around his neck. Mr Tovares is quivering with fright, and grasps my hand to his chest when I greet him.

Major John Mcaffrey, in charge of the checkpoint, gestures to the refugee's bundles of possessions – a cooking pot, old wooden bed heads, cane sleeping mats, a plastic stool, oil lamp, plastic jerry cans and a grubby tooth brush. One whiskered old man nurses a hen cradled in a sarong slung off his shoulder.

"A lot of refugees coming across say the militia stole everything of value," Major Mcaffrey says. "Others bring an Indonesian army flag as a safe pass to get through militia roadblocks, then they pull them out and drop them in the river before they get here.

"Quite a few have malaria and dengue. Some have bruises from beatings, and are absolutely terrified." By late morning officials from the United Nations High Commissioner for Refugees are taking names and registering the refugees. They begin to relax when told that trucks will soon arrive to collect them and they will be home within 24 hours.

The Malibaka crossing, one of six authorised crossing points between East and West Timor, is heavily guarded by Australian troops. Major Mcaffrey says cooperation with the Indonesian military on the other side of the river has been good.

The Indonesian soldiers are from 502 Airborne Battalion, a unit that once trained in Australia. There is a direct phone link to the Indonesians, who used the connection early yesterday to alert the Australians that the refugees were on the way.

"They are proud to wear their parachute wings, and were not mixed up in last year's violence," Major Mcaffrey says. "I think they want to show that they were not part of it."

He says there is some evidence the Indonesian army is losing its patience with the militias. Two days ago, a notorious militia leader, Armindo Soares, was seen at the nearby Nunura Bridge checkpoint being beaten up by refugees in circumstances that are unclear. Indonesian soldiers arrived on the scene to restore order and also began kicking the man before leading him away.