HMAS Glenelg on Sunday night intercepted a boat carrying 37 asylum seekers and four crew near Ashmore Island.
The interception followed an earlier sighting of the boat by a Customs and Border Protection air patrol.
Another asylum seeker boat carrying 41 passengers and three crew was intercepted on Monday by HMAS Broome near Christmas Island.
It was the 32nd asylum seeker boat intercepted in Australian waters this year.
Both groups will be transferred to Christmas Island for security, identity and health checks. Their reasons for travel will also be established.
Over the weekend, the government came under fire from the Opposition after a group of asylum-seekers were transferred from Christmas Island to Sydney, because the centre was reportedly too full.
