The iron-ore train derailed following torrential rain in the Northern Territory caused by Grant, a tropical cyclone that triggered heavy flooding in some areas, swamping roads and stranding scores of people, police said.
Its two crew members both managed to escape and were assessed by medical staff who were helicoptered to the scene, with the driver later airlifted to hospital with spinal injuries according to local media reports.
"The (Australian Transport Safety Bureau) has been notified of the crash and will take carriage of the investigation," Northern Territory police said in a statement.
Local government official Willem Westra Van Holthe said it appeared as though the train had come off the tracks while attempting to cross the waterlogged bridge, with an "enormous amount of water flowing across the road".
"It's what I'd describe as a scene of devastation here," he said.
"The whole scene is quite shocking."
Westra Van Holthe said freight carriages were being carried downstream and "there's sheets of bitumen that have been lifted off and carried away".
"I've lived in the Territory for 27 years and I've never seen anything like it," he told the Northern Territory News.
Police said another two people were "lucky to be alive" after their car stalled on the same bridge a few hours before the train derailed and they were swept from the car's roof.
"They were able to grab hold of a tree about 50 metres downstream and waited until help arrived," police said.
Grant was downgraded to a tropical low on Monday but the weather bureau said it could hit cyclone strength again on Thursday as it moved off land and across the warm waters of the Gulf of Carpentaria.
Heavy rains and high tides were expected in the meantime, with minor flooding likely in some areas.
Cyclones are common in northern Australia during the December-February summer. A series of storms unleashed record floods across Queensland state last January, killing dozens of people and battering the economy.
-AFP