Derailed NT train contained toxic chemical

The company that operates a train that derailed in Northern Territory floodwaters is investigating the damage as environmental authorities focus on a possible chemical spill.

Footage of the incident posted on YouTube - SBS cannot verify its accuracy.

Further footage of the incident posted on YouTube shows discoloured water at 1:13 - SBS cannot verify its accuracy.

The freight train came off the rails near the Edith River bridge about 40km north of Katherine early on Tuesday morning, when floods caused by Cyclone Grant washed away part of the bridge.

The accident has raised concerns that hazardous chemicals carried by the train have leaked into the rain-swollen river.

Genesee and Wyoming Australia (GWA) confirmed in a statement on Wednesday that two of the 33 wagons contained copper concentrate.

A spokeswoman for GWA said it was too early to comment on any possible spill.

"Yesterday they were only able to do an aerial assessment ... so they don't know the full extent of the damage to the train," she told AAP.

A spokeswoman for the Department of Natural Resources and Environment (NRETAS) said staff were currently investigating the spill and prosecutions could follow if any negligence was found.

"We're taking it pretty seriously," she said.

"There will be a thorough environmental investigation."

Both NRETAS and GWA said they expected to have more information later on Wednesday.

Meanwhile, one of two crew members injured in the crash continues to recover in hospital.

GWA said in a statement the stretch of rail between Katherine and Darwin remained out of service.

"Crews are inspecting the bridge and making plans for restoring service over the approximately 350-metre affected segment.

"It is not yet known how long repairs will take."

GWA operates the 2200km rail line between Tarcoola and Darwin, which links the Port of Darwin with the Australian interstate rail network in South Australia.