About 4.30am AEDT this morning, AMSA detected an unregistered distress beacon 166km east of Darwin near the Alligator Rivers region in Arnhem Land.
AMSA tasked its Darwin based dedicated search and rescue Dornier aircraft and a Careflight rescue helicopter to respond.
On arrival at the site of the original beacon detection, two large eskies were seen floating in the water.
The strobe light of the distress beacon was then seen on nearby mud flats and two men were located about 6.40am AEDT.
It is understood the men's boat sank early this morning and the men were able to swim to the mud flats.
AMSA strongly encourages people to register their distress beacon. Registering your beacon means AMSA can contact you or an emergency contact if your beacon is activated and determine the nature of distress and your location, and help to ensure help arrives as soon as possible.
Registering your beacon is free and only takes a few minutes and can be done online or by phoning 1800 406 406. Trip details can also be logged, as well as a photo of your vessel.