Separately, another 18 asylum seekers from Sri Lanka were returned home, The Sydney Morning Herald reported.
The naval ship and a number of merchant ships picked up the 180 asylum seekers in the Sunda Strait about 60 miles off the coast of Indonesia, a spokesman for the Australian Maritime Safety Authority said.
The asylum seekers aboard the naval vessel will be taken to Christmas Island, the spokesman said. The destination for those about the merchant vessels was unknown.
The Sri Lankan men, who had been detained on Christmas Island, flew back to Colombo Saturday after they refused to be sent to Nauru for processing, the Melbourne Sun Herald reported.
The Australian government said it considered both incidents to be victories for the country's immigration policies.
"Both the Nauru transfers and this group of adult Sri Lankan men choosing to return home provide further evidence that the people smugglers are selling lies and misleading asylum seekers about the situation they will face if they reach Australia by boat," Immigration Minister Chris Bowen said.
More than 2,000 asylum seekers have arrived by boat since Australia announced in August that all asylum seekers would be processed 2,600 miles from Australia in the island nation of Nauru.