The Australian Navy has transferred dozens of asylum seekers to Indonesian authorities during a rendezvous off the coast of Java.

The 44 asylum seekers and two crew members were on a boat which got into trouble 40 nautical miles off Java yesterday morning.

Suyanto, the head of operations at the Jakarta office of Indonesia's rescue agency Basarnas, says his agency did not have the capability to reach the stricken boat.

The Australian Navy intercepted the vessel and then advised Indonesia that it would drop the asylum seekers off.

In the early hours of this morning an Indonesian rescue crew met a Navy ship off the coast of Java and the asylum seekers were handed over.

Suyanto says he does not know why Australia did not take the asylum seekers to Christmas Island.

More to come.