NT WorkSafe has ordered OZ Minerals to remove copper concentrate from the Edith River following a train derailment late last month.
The train reportedly went into the river after flash flooding wiped out sections of the track.
Around 1200 tonnes of copper concentrate washed from the train into the river after a flash flood on 27 December.
The train was travelling north to Darwin at the time.
Two employees from Genesee and Wyoming Australia (GWA), which operated the train, were safely evacuated.
Following the incident, OZ stated that "given the large volume of water flowing through the system it is likely that any concentrate that has been impacted by the would be highly diluted".
OZ Minerals has been ordered to remove the remaining concentrate and to facilitate the clean up of the river.
However, any copper concentrate found which is not in the immediate vicinity of the derailment is not subject to the orders, NT WorkSafe added.
Despite fears raised of the potential for traces of uranium to be washed into the river along with the concentrate, the Northern Territory Government gave the river the all clear following testing.
It stated that the low to moderate amounts of copper, zinc and aluminium detected at test sites were "well below health guideline values", the NT News reported.
"Testing did not detect uranium at any of the four testing sites," the Government statement said.
Despite this, the Greens are up in arms over the incident, saying that it raises a cloud over the environmental assessment for the Olympic Dam expansion.
Since the use of this rail line is critical to BHP’s massive Olympic Dam expansion, Tony Burke needs to urgently reconsider his approval of the project in the light of new concerns," Australian Greens acting leader, Senator Christine Milne, said.
"A spill of toxic copper concentrate into the central Australian environment is bad enough, but Olympic Dam would be a radioactive disaster waiting to happen.
"What different conditions from those approved for the toxic copper concentrate transport did Minister Burke require for the transport of uranium oxide across the country? If none, then the Minister has placed both the environment and local communities at great risk and needs to immediately recognise just how dangerous mining and transport of uranium is, and reconsider immediately.
"The private operators of this rail line apparently thought that sending a four wheel drive across the bridge seven hours earlier was sufficient testing before the train came through. Clearly this is not reasonable and cannot be sufficient if uranium oxides are transported along the line."
Since the incident, OZ Minerals has ordered new containers to transport the spilled materials.
OZ spokesperson Rachel Eaves said "they could be considered beyond compliance as they are developed to load a bulk commodity without the use of a ship loader".
According to the miner, the total value of the concentrate was between US$7-8 million.
The crossing bridge over the Edith River is expected to re-open this week, with the rail line repaired by the end of the month, the ABC reports.
Image: News.com.au – Michael Franchi