UPDATE 11.50AM TUESDAY: 

Authorities have detained two illegal fishermen as they attempted to cross the Daintree River on board the ferry, ending the three-day drama of an alleged Vietnamese people smuggling operation involving 17 people.

About 15 members of the sunken fishing trawler are already on their way back to Vietnam, with Border Force  questioning the two men caught today over their involvement in a possible people smuggling network.

Home Affairs Minister Peter Dutton told reporters the boat was the first to reach Australia in more than 1400 days.

EARLIER: The croc-infested Daintree River is proving to be a natural 'border force' helping authorities round up a group of Vietnamese fishermen on the run in the rainforest.

About 15 crew members of the sunken fishing trawler have now been captured by officers from Australian Border Force and Queensland Police, with some of the men caught near the Daintree Ferry earlier today - the only safe option for the men to cross the river.

But details remain sketchy about how many of the crew are still missing.

A spokesperson from the Department of Home Affairs declined to provide details on the operation, issuing the following statement: 

"The Australian Border Force is currently investigating what we believe to be an illegal fishing vessel that ran aground north of Port Douglas.

"The ABF has a contingent of officers on site and is grateful for the support being provided by Queensland Police Service. We can confirm that a number of potential unlawful non-citizens have been located.

"The ABF and Department of Home Affairs will undertake the necessary border processes to establish circumstances around the arrival. As investigations into this matter are ongoing it would be inappropriate to comment further."