"The group will be transferred to Christmas Island, where they will undergo security, identity and health checks," O'Connor said in a statement.
"Their reasons for travel will also be established.
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Hundreds of asylum-seekers have been picked up by Australian officials this year after risking perilous sea voyages, re-igniting the country's fierce immigration debate.
The government of centre-left Prime Minister Kevin Rudd has said that unrest in countries such as Sri Lanka and Afghanistan is behind the spike in the number of boatpeople arriving here.
But the conservative opposition has said the government's softening of the previous administration's immigration rules had opened the way for the increase.
On Thursday, border guards stopped another two boats carrying 56 people, while Indonesian officials last week intercepted a group of 2