HMAS Wollongong found the vessel on Tuesday night, west of WA's Cape Leveque.
Home Affairs Minister Brendan O'Connor says the vessel's been under surveillance by Border Protection Command for several days.
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He says the 46 passengers and two crew members will be taken to Christmas Island for security .. identity and health checks.
O'Connor said the vessel was initially detected by a Customs and Border Protection Dash 8 aircraft, operating under the control of Border Protection Command.
"Initial indications suggest 46 passengers and two crew members are on board the vessel," he said in a statement.
"The group will be transferred to Christmas Island where they will undergo security, identity and health checks."
Their reasons for travel will also be established."
If those aboard are from Afghanistan or Sri Lanka their claims for asylum will be delayed for at least three months following a change of government policy earlier this month.
"Their claims will not be considered until these suspensions are lifted," Mr O'Connor said.
