An environment group says the derailment of a train carrying hazardous substances raises concerns about the transport of uranium through the Northern Territory.

A freight train transporting containers of copper concentrate was derailed yesterday after flash floods damaged the railway track north of Katherine yesterday.

The Environment Department is investigating reports that containers may have spilled and washed into the Edith River.

Environment Centre NT director Stuart Blanch says the incident is a worrying sign.

"This spill highlights a lack of due diligence by the owners of the railway and the people transporting this product," he said.

"What would have happened to the Edith if there was a spill of uranium oxide into the Edith River?

"That is a real concern, with a lot more uranium coming up from South Australia in the years ahead."

Meanwhile, Chief Minister Paul Henderson says he is satisfied that copper concentrate was the only toxic substance being carried by the train.

Mr Henderson says it is not radioactive material from a uranium mine in South Australia.

"What the environmental impacts may be, I have not been briefed as to what they may be," he said.

He says government officials are on site to carry out a monitoring program.