Two men have been found clutching to a tree above a crocodile-infested river, hallucinating, covered head to toe in mosquito and midge bites, after their boat partially sank in Kakadu National Park.

Key points: The two men were found clinging to a tree, severely dehydrated and covered in insect bites

The two men were found clinging to a tree, severely dehydrated and covered in insect bites Their boss chartered a helicopter to search for the pair after they failed to arrive at work

Their boss chartered a helicopter to search for the pair after they failed to arrive at work The men were transported to Royal Darwin Hospital and are both in a stable condition

When two employees did not show up to work after a fishing trip, a quick-thinking Territory boss chartered a helicopter to search for them.

Those actions likely saved the lives of the two men in their 20s, who had spent two days clinging to the branches of a tree over the South Alligator River when the chopper went past.

The pair had been fishing when their boat partially sank, forcing them to climb into a tree.

They were able to signal to the passing helicopter using a fire extinguisher, who alerted CareFlight who were able to get a rescue operation underway.

CareFlight doctors treated the men for dehydration. ( Supplied: CareFlight )

Fire extinguisher used to gain attention

CareFlight spokesperson Elliana Lawford said the fire extinguisher was the only thing the men were able to grab from the boat before it became inundated with water.

"They started shooting it into the air and on the third time the helicopter spotted it," she told ABC Radio Darwin.

What might seem like a strange thing to grab may have saved their lives.

"Our aircrew officer said it was a genius idea ... it let off so much chemical smoke," Ms Lawford said.

Rangers and friends helped the men to a carpark near the South Alligator boat ramp, where they were collected by the CareFlight team.

"Unfortunately, when we arrived they were suffering from extreme dehydration, they had been having hallucinations, so our doctor essentially provided some treatments to rehydrate them," Ms Lawford said.

"They were covered head to toe in midge and mosquito bites, as you can imagine from being stuck in a tree on the South Alligator," she said.

The men were airlifted to Royal Darwin Hospital in a stable condition.