Authorities have detained 15 people and think more are hiding in mangroves north of Cairns, say police.
The boat, believed to be from Vietnam, is the first people-smuggling vessel to make it to Australia "in more than 1,400 days", according to Home Affairs Minister Peter Dutton.
Authorities are continuing a search.
They did not say how many people were aboard when the boat ran aground near Daintree on Sunday, nor if any have plans to appeal for asylum.
Local mayor Julia Leu told ABC that they were "putting themselves at risk in known crocodile habitat".