A young man has had his new four-wheel drive dragged almost a kilometre by a freight train after trying to cross a track in the Northern Territory.

Police said about 1:00am on Sunday a 23-year-old man was driving through bushland following a friend in another four-wheel drive when the pair attempted to cross the Adelaide to Darwin rail line near Katherine about 315 kilometres south of Darwin.

Duty Superintendent Louise Jorgensen said the men picked a "non-designated crossing" as the spot to drive over the rail line.

"One car has made it across, but the vehicle driven by the 23-year-old has become stuck on the tracks," Superintendent Jorgensen said.

"The men attempted to free the vehicle but were unable to do so."

Superintendent Jorgensen said when a Darwin-bound, kilometre-long freight train carrying manganese approached, with the men shone torches and waved to try and get the attention of the driver.

The lead locomotive dragged the 4WD vehicle about 500 metres down the Adelaide-Darwin rail line. ( Supplied: NT Police )

The train driver attempted to slow the train but collided with the vehicle, dragging it about 500 metres under the lead locomotive, coming to rest over a rail bridge.

The two men were able to jump to safety and were uninjured.

The train driver was treated for shock and taken to Katherine Hospital for observation. He was released about 6am today.

"It's happened before, people trying to cross at non-designated crossings, which people should never do," Superintendent Jorgensen said.

Superintendent Jorgensen said the recovery operation could take hours, with the lead locomotive "inoperable".

The men, understood to be Katherine locals, are expected to face a number of charges over the incident.

"There was no alcohol involved," Superintendent Jorgensen said.

'Young idiots' could have killed crew

The wreckage of the 4WD is recovered from under the freight train in Katherine. ( ABC: James Oaten )

Train operator Genesee and Wyoming general manager Greg Pauline was at a loss to understand the two men's actions.

"I'm a bit upset about it," he said.

"These young idiots could have killed themselves or my crew."

He said a goods train carrying groceries to Darwin was behind the freight train, with delays expected for several hours.

"It shouldn't affect our network too much," he said.

Mr Pauline said he understood the man's vehicle was uninsured.