A group of asylum seekers was intercepted off the north-west coast of Western Australia on Sunday morning.
They are the first group to arrive since the signing of a swap deal with Malaysia on Monday.
HMAS Ararat detected the boat north-west of Scott Reef.
The ABC reports they are expected to be sent to Malaysia.
Home Affairs Minister Brendan O'Connor said initial indications suggest there were 54 passengers and two crew on board.
Immigration Minister Chris Bowen told Sky News the group will be processed in coming days.
Under the refugee swap deal, Australia will send 800 asylum seekers to Malaysia and accept 4000 verified refugees in return.
Transferred asylum seekers will receive no preferential treatment in the processing of their claims.
Last group being processed
The last group of asylum seekers to be processed under Australia's old immigration policy was taken to Christmas Island on Saturday.
The group of 47 is believed to be from Afghanistan, Iraq and Iran.
The ABC reports their boat was intercepted last Sunday, before the swap deal with Malaysia came into effect on Monday.
The Immigration Department says any asylum seekers who arrive by boat in future will be flown to Kuala Lumpur within 72 hours of arrival.
