Indonesian authorities warn that an influx of up to 10,000 refugees is expected to head to Australia.
About 1500 asylum seekers have already arrived in Indonesia from Malaysia by boat this year and registered for refugee status.
Fairfax newspapers report the same number again are believed to have arrived and not registered. They are believed to be from Afghanistan, Sri Lanka, Burma and Iraq.
Malaysia is used as a staging point to obtain tourist visas before refugees seek passage to Australia via Indonesia.
The United Nations High Commission for Refugees has 49,000 registered refugees and asylum seekers in its records in Malaysia. It estimates there are 45,000 unregistered illegal immigrants.