Two boats carrying more than 100 people have been intercepted in Australian waters since Christmas Day.
A vessel was discovered east of Ashmore Islands on Tuesday by HMAS Wollongong, AAP reports.
Initial reports suggest there were 95 passengers and three crew on board, Customs and Border Protection said in a statement.
In a separate incident, HMAS Maryborough detected and intercepted a vessel north of Christmas Island on Boxing Day.
There were believed to be six passengers and two crew on board.
Arrangements were being made for the passengers from both vessels to be transferred to Christmas Island.