Energy Resources of Australia Ltd (ERA) has rejected suggestions the company is mining by stealth and using ore from an exploration tunnel at its Northern Territory Ranger mine.

ERA, one of the world's biggest uranium miners, has been accused of planning to mill a bulk sample of 30,000 tonnes of uranium ore from the exploration tunnel without environmental approvals.

The tunnel is part of the company's 3 Deeps project, which ERA hopes will prolong the life of the open cut Ranger mine in Kakadu National Park by mining underground.

On Wednesday the Environment Centre NT and the Australian Conservation Foundation put out a joint statement saying ERA wanted to extend its exploration tunnel by one kilometre and start a small milling operation using a bulk sample from the debris.

Dr Gavin Mudd, an environmental engineer from Monash University, said Ranger 3 Deeps being converted to a small mine made a mockery of the principles of environmental assessment.

"It is a very murky zone about whether it is mining or not," Dr Mudd said.

"I understood that there would only be a tunnel, and any mineralised material found while tunnelling, that ore would be stockpiled and not touched," he said.

"That was the commitment."

But ERA chief executive Rob Atkinson rejected claims his company was planning on mining the 30,000-tonne sample.

He confirmed the company may seek to extend the exploration tunnel from the current 2.2km to a possible 3.2km, but said a mine operation using the relatively small amount of debris from the tunnel was nonsensical.

"Any suggestion that we are doing this under a cloak of darkness or a cloak of secrecy is just nonsense," he said.

He said the current exploration plan did not involve processing any uranium.

If the company did decide to use a bulk sample to test equipment at the mine it would seek new approvals beforehand, he said.

The underground operation is projected to begin operating in 2015/16.