Stephen Fitzpatrick, Jakarta – Indonesian police have moved to treat all asylum-seekers passing through the country on their way to Australia as potential terror suspects.

The new approach comes with help from the Australian Federal Police, who have helped Jakarta to build a computer database that can cross-check illegal immigrant and terrorism arrests.

The database was expected to be operational by next month, the country's most senior police officer in charge of transnational crime told The Australian.

Brigadier General Saud Usman Nasution said at least one recent people-smuggler arrest in Indonesia had suggested a direct link to international terrorism, possibly al-Qa'ida. The arrest was in the Sumatran city of Medan and the smugglers involved were still being held in custody, General Nasution said.

"From their communication, from their phone numbers, we opened their phones and then there was some talking about terror," he said. "We tried to follow from their phones. We tried, with the AFP, to open this communication, and we are sharing the information with the AFP."

He said the case was the first time people-smugglers in Indonesia had been clearly linked to international terror networks, and warned that the development was ominous.

"I think they (terrorists) will always change their modus operandi, and will come to areas with a new cover as an asylum-seeker," General Nasution said. "If they come as an asylum-seeker, it's not easy for us to arrest them, because we have no data about them."

He said terrorist agents could have already made it to Australia as asylum-seekers.

General Nasution said the AFP was helping to build the database, which could cross-match fingerprints, photographs and testimonies of all foreigners arrested in Indonesia. It would be accessible at 16 provincial police headquarters deemed the most likely crossing-points for asylum-seekers heading to Australia.

General Nasution said the system was designed to be able to share data with the countries of origin of illegal immigrants detained in Indonesia.

Although Australia had been helpful in its short-term approach to dealing with the asylum-seeker issue, the longer-term threats to Indonesia's security remained worrying, he warned.

Any prospect of Australia turning asylum-seeker boats around on arrival could never be supported by Indonesia. "In the UN convention, it mentions we cannot refuse for asylum-seekers to come to our country – and this includes Australia."

Jakarta is not a signatory to the UN convention, but a tacit agreement with the world body allows it to process refugee applications in-country and then transfer successful applicants to third-country signatories to the convention, including Australia.

[Additional reporting: Paul Maley.]