Another two vessels carrying asylum seekers were intercepted by the Australian navy off Christmas Island on Thursday night.
One of the vessels was carrying 66 people and was intercepted in international waters about 100km north of Christmas Island.
The other, initially thought to have 60 people onboard, was north-west of the island.
The ABC reports a further 50 people, 49 asylum seekers and one crew member, were found on the boat under a second hidden deck.
It is understood the boat in international waters needed assistance and a search involving an Australian aircraft and ships was coordinated by Indonesian authorities.
HMAS Pirie found the boat about midnight on Thursday AEST.
The second boat was intercepted by HMAS Albany early on Thursday morning after it was detected by an RAAF aircraft.
The asylum seekers are being transferred to Christmas Island.