Border Force say the group was on a suspected illegal fishing vessel, but it's not clear whether those on board are lost fisherman or asylum seekers.
Home affairs minister Peter Dutton said: "Australia, we believe, has received the first. people-smuggling venture in over 1,400 days".
It could not confirm how many others may have been on the boat.
About 40 people are thought to have been on board, reports say.
Federal Member for Leichhardt Warren Entsch, whose electorate covers the area where the boat arrived, dismissed the speculation and instead said he believed the crew were illegally fishing in the area when they ran into trouble.
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There are warnings about crocodiles in the area near the Daintree River ferry crossing in far north Queensland.
The last asylum seekers to reach Australia by boat were six Chinese nationals travelling from Papua New Guinea, who landed in Saibai island in north Queensland in August of a year ago.
"We need to make sure firstly that the people are safe in place, and then we can start the process of deportation as quickly as possible".
Local Mayor Julia Leu told ABC there was concern that people were "putting themselves at risk in known crocodile habitat". 7 News understands locals helped bring the vessel ashore as the asylum seekers fled into rainforest at Cape Kimberley just north of the Daintree River.
One Nation leader Pauline Hanson has suggested those on the boat may have headed for Australia as a result of last week's leadership crisis in Canberra. Asylum-seekers who try to reach Australia by boat are either turned back or sent to remote Pacific camps where conditions have been widely criticised.
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Even if found to be refugees, they will never be offered resettlement in Australia - a controversial policy created to deter future arrivals.
"Because the eye was off the ball last week and the news would have happened that Malcolm Turnbull is no longer Prime Minister and these people would have come on a boat to Australia".
MP George Christensen has since taken to social media to call for better border protection.
Paramedics in Mossman treated two people in custody for fever and chills.
If the boat were carrying asylum-seekers, it would be the first time in four years that such a vessel has reached Australian shores. "Qld borders need to be made more secure esp given proximity of PNG & Indonesia, considering level of radical Islamism in Indonesia, Malaysia & Philippines", he tweeted.
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Several people are said to have been detained, The Courier Mail reports, while the rest are believed to have fled into the Daintree Rainforest.