Rail operator Genesee and Wyoming says clean-up efforts are nearly complete at the Edith River crossing where a train derailed in December, spilling tonnes of freight and copper concentrate.

A number of train carriages and freight containers were swept in to the Edith River, north of Katherine, during flooding associated with a tropical cyclone.

Genesee and Wyoming says approximately 920 kilograms of damaged infrastructure and loose freight has now been recovered from the site.

Four skip bins of debris and five cubic metres of plastic were also taken out and disposed of in landfill.

The company says all freight containers except one have been removed.

The Northern Territory Department of Environment says any items left in the river will be removed following scheduled burning-off in the area.

Investigation of the train derailment is continuing.