One boat carrying 123 passengers was found east of Christmas Island while the second sailed directly to Cocos Island from Sri Lanka with 36 people on board.
Passengers on the Sri Lankan boat will be flown to Christmas Island for processing, with two charter planes in the past week moving other asylum seekers from Cocos Island.
In just over three weeks this month, 1278 people have arrived on boats.
In the past 10 days, the Immigration Department has spent almost $5 million flying asylum seekers to detention centres around the country.
More than 5100 asylum seekers have been flown off Christmas Island this year to prevent overcrowding.