A group of fishermen were forced to ride out a thunderstorm in a broken boat that was being repeatedly rammed by a crocodile in remote Northern Territory before being rescued by Daly River Police.

Key points: Three men were rescued from the Daly River after drifting for more than seven hours

Three men were rescued from the Daly River after drifting for more than seven hours Their boat engine had broken down

Their boat engine had broken down Police said there was some doubt if some in the group would go fishing again

It was the first time on a boat for one of the men, who radioed the Australian Border Force for help during the ordeal.

The men, aged 37, 29 and 27, set out to go fishing on Wednesday afternoon on the Daly River — a river system notorious for its crocodile population with more than 50 filmed sunbathing earlier this year.

Duty Superintendent Bruce Payne said they were soon faced with trouble when they hit a sand bar, damaging the water pump and overheating the motor.

After springing back to life and setting them on course back to the Daly River Boat ramp, the motor then died completely and they were left adrift.

Superintendent Payne said the men then radioed Border Force, who relayed their predicament to NT Police.

"The party had to deal with a severe thunderstorm, an aggressive crocodile and they also then struck a submerged object that almost caused their boat to capsize," Superintendent Payne told ABC Radio Darwin.

They activated their EPIRB at about 7.40pm.

Acting Senior Sergeant David Young said the fishermen were not in the reported location, and it took Daly River police officers until just after midnight to find them with marine spotlights.

Police said there was some doubt whether the first-time fisherman would ever go out again.

"It was a pretty traumatic experience for these men, one of whom had never been on a boat before," Acting Senior Sergeant Young said.

"Nearly everything that could go wrong did go wrong, but luckily these men have lived to tell the tale."

He took the opportunity to remind other anglers that conditions can change quickly at this time of year, and that they should carry an EPIRB and enough food and water.

"They were quite shaken up by their experience," Superintendent Payne said.

"[I] can't overstate the importance of the EPIRB. It was extremely valuable in this instance."

Sorry, this video has expired Crocodiles on the Daly River ( Supplied: Wade Kelly )

Just before Christmas, another group of fishermen were left stranded on the South Alligator River when they ran out of fuel.

They waited two days before turning on their EPIRB, when the onset of dehydration became too much.

Days earlier, four fishermen were rescued after their boat capsized in Top End Waters.

One of the men was missing for two days before he was found.