The boat carrying 54 passengers and two crew was stopped in international waters by border patrol officers following a tip-off from an oil rig, said Home Affairs Minister Bob Debus.
Those on board were taken onto a navy ship, he said in a statement.
The vessel was intercepted about 900 kilometres (560 miles) north of Darwin city near Ashmore Island, the site of a blast on board a people-smuggling vessel on April 16 which killed five Afghans and injured dozens more.
Saturday's vessel was the eighth to be intercepted off Australia or to have made landfall since January, carrying hundreds of refugees from the subcontinent and Afghanistan.
The ethnicity of the most recent arrivals was not immediately known.
Debus has warned of "thousands" of illegal immigrants waiting in Indonesia for passage to Australia, with a boat carrying 32 Sri Lankan refugees stopped near the northwest coast on Thursday.
Canberra had dispatched a delegation to Malaysia and Sri Lanka for high-le