Police received a report about 5.30am that the iron ore train derailed just north of Edith Falls River Crossing.

"Police have now also reached the scene of a freight train derailment north of Edith Falls River Crossing," Commander David Proctor said.

"The driver and co-driver are being medically assessed after having walked to the Stuart Highway. The ATSB has been notified of the crash and will take carriage of the investigation."

The pair will be taken to the Katherine District Hospital.

Police would like to reinforce to motorists that the Stuart Highway is closed to the South from Pine Creek and they should not attempt to travel until advised that the Highway is reopened.

"Police believe the train has about 20 carriages and the incident has led to a complete derailment," the commander said. "We need to ensure the scene is safe before investigations can begin into how the freight train came off the tracks."

Katherine MP Willem Westra Van Holthe told the ABC the Edith River Bridge has collapsed and carriages are floating downstream.

"It's what I'd describe as a scene of devastation here," he said. "Apart from the enormous amount of water flowing across the road, there's sheets of bitumen that have been lifted off and carried away and also it appears as though the train tried to get across this morning while the river has flooded.

"The train bridge appears to have collapsed."