Indonesian police say there is mounting evidence military personnel were involved in arranging the boat which capsized last month, killing around 200 asylum seekers.

Indonesian and Australian Federal Police are investigating the sinking of the overloaded boat, which went down about 40 nautical miles off East Java with around 250 asylum seekers on board.

The boat was reportedly en route to Australia.

Shortly after the sinking, three soldiers were detained and accused of organising the final stages of the voyage. A civilian defence employee was also arrested.

But ABC TV's 7.30 has learned the military's involvement in the smuggling has become a widening scandal as two more soldiers have been implicated and brought in for questioning.

The military command in East Java, led by Major-General Murdjitok, has pledged full cooperation.

"Who wouldn't be unhappy to uncover the syndicate? That's what we are trying to do right now," he said.

"We need complete and comprehensive coordination, but for the time being, we are dealing with our people."

But Indonesian police fear they will be blocked from pursuing inquiries which lead up the chain of command.

They say the soldiers are being held by military police and most of the progress in the case has come from civilian investigators.

Investigators argue the low-ranked soldiers are unlikely to have been involved without the consent of their superiors, who were probably also paid.

Macabre identification

Meanwhile, survivors and relatives of those who died in the disaster have spoken of their frustrations at not being able to identify those who perished.

While 103 corpses were recovered from the disaster, only 23 have been identified and now Indonesian authorities say they will bury the rest in less than a week.

The bodies are now being stored in a shipping container with intermittent refrigeration.

The victim ID teams have resorted to posting up pictures of items recovered from the dead in the hope a family member will recognise something decisive.

Ali Poya, a Hazara refugee who has made his life in Perth, is still looking for his two cousins, but he identified his brother Azatula thanks to a macabre slideshow on the computer.

"I saw the pictures they pull out from his pocket, you know, from his property," he said.

"I saw my dad's picture and I saw his daughter's picture as well and I saw some numbers that match up with my family and I'm sure he is my brother's body."

Habib Isaac, a Hazara refugee living in Adelaide, is another engaged in this agonising search.

He has identified four cousins but the fate of three others remains a mystery.

"It is so undignified. Every time, every day, they open the gate and the smell of the dead bodies goes all around the hospital and you know that your loved ones are in that container and they are actually suffering," he said.

Other survivors have also complained of beatings from guards at the detention centre where they are being held.

Ali Mohammad and his friends broke out, determined to find another boat to Australia despite the risks.

But Mr Mohammed was recaptured and as his mobile phone footage shows, he was bashed before he was brought back to his cell.

"The immigration officers and local people, they fastened my wrists and my feet as well. Then they hit me with a baton on my head while bringing me through the front gate," he said.

The camp guards say the detainees are dangerous and violent. The head of the detention centre declined an interview.