The operator of the Ranger uranium mine in the Northern Territory has now revealed three cases of water contamination.

The mine, which is surrounded by the Kakadu National Park, was shut down on Wednesday after it was discovered that process water leaked into the mine's drinking water system.

Energy Resources of Australia says the contamination appears to have been caused by a false connection between the mine's process water system and the drinking water system on Tuesday night.

The company has revealed it cannot rule out the possibility that it has happened before.

The Federal Government's supervising scientist is investigating the environmental impact of a third contamination incident.

Dr Arthur Johnston says process water from the mine overflowed from a holding tank near the Jabiru Airport on Tuesday night.

He is concerned about traditional owners downstream because of the possibility that contaminated water has entered the water table that feeds into Kakadu.