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An army officer facing charges over one of Indonesia's worst asylum seeker boat disasters has been accused of playing a key part in organising the ill-fated venture.

Five soldiers were arrested in December last year after they were linked to an asylum seeker boat which capsized in rough monsoonal seas on its way to Australia within hours of leaving from a port in East Java.

As many as 200 asylum seekers drowned when the overloaded boat sank on December 17.

Just 49 people survived the disaster.

While members of Indonesian military have been implicated in people-smuggling cases in the past - including as recently as two weeks ago - their roles are commonly limited to acting as escorts.

But a military court hearing next week in Madiun, East Java, will hear allegations that at least one of the officers arrested over December's tragedy was heavily involved in arranging the doomed voyage.

Sergeant Ilmun Abdul Said is accused of helping to obtain the vessel from local fishermen and advising people smugglers on where to launch the boat.

The commander for Brawijaya Military Police, Colonel Budi Purwono, who oversaw the investigation, has told AAP that Sgt Said also recruited the other four officers to help send the boat to Christmas Island.

“These officers were being used by civilians to help send people over the ocean,” Col Purwono said.

Sgt Said's brother was the key link in the chain between the people-smuggling syndicate and the TNI officers.

“After his talks with his brother, who told him that there were people who wanted to cross the ocean, then he asked around to see who was willing to help,” Col Purwono said.

“He also helping them to get the boat and telling his brother which area on the coast it was possible to use.”

The identities of those in charge of the syndicate have not been revealed, although at the time of the disaster, people-smuggling kingpin Sayed Abbas was linked to the venture.

Abbas is currently detained in Indonesia, and the Australian Government has made it clear in the past that it would like to extradite him to face people-smuggling charges.

The trial of Sgt Said comes as another group of soldiers remain in custody after they were caught last month escorting a group of asylum seekers to the southeastern coast of Java - a popular disembarkation point for boats heading to Australia.

Sgt Said could be jailed for up to 15 years if convicted of people smuggling.

He also faces a number of other charges and dismissal from the army.

The other four soldiers will face court at a later date.