The traditional owners of the Ranger uranium mine in the Northern Territory say a contamination incident has exposed Aboriginal communities to an unprecedented threat.

Energy Resources of Australia (ERA) shut the mine on Wednesday after it was found the drinking water was contaminated.

ERA says it cannot rule out the possibility that it has happened before.

The Federal Government's supervising scientist is also investigating another incident where process water overflowed from a holding tank into a nearby creek.

The Gundjehmi Aboriginal Corporation has issued a statement saying the spill puts Kakadu ecosystems at risk, along with the health of Aborigines who live and hunt nearby.

Meanwhile, Dave Sweeney from the Australian Conservation Foundation says the situation at the Ranger mine is unacceptable.

"We hear now of tens of thousands of litres of contaminated water flowing into areas and catchments for the feeder creeks for the wetlands of Kakadu, what we have is a horrible week for Energy Resources of Australia and a horrible week for the people and environment of Kakadu - it's completely unacceptable," he said.