Radioactive water is in danger of spilling into an Aboriginal community and Kakadu's World Heritage-listed wetlands if record rainfalls continue to deluge the vast Ranger uranium mine.

Mine management faces drastic action to avert an environmental disaster and avoid costly delays that could stall high-grade ore extraction for months or even years.

Rio Tinto-controlled Energy Resources of Australia relies on the Ranger mine, 230 kilometres south-east of Darwin, to supply 10 per cent of the world's uranium market, including Japan's stricken Fukushima plant.

ERA will be forced to pump more than 10 billion litres of highly contaminated water from an almost overflowing dam into its operating open cut mine, known as Pit 3, if the Kakadu area receives about 100 millimetres more rain.

This level of rainfall is likely with three weeks of the Top End's wet season still remaining.

The company conceded this week it will not be able to resume production in the pit until the end of July at the earliest and that its "ultimate contingency" to protect the environment is to transfer water from the tailings dam.

But Pit 3 - the only place available to put the water - already contains 3.6 billion litres of water that is sitting above high grade ore deposits.

If forced to pump water containing heavy metals and radioactive material from the tailings dam into the pit, ERA would then have to treat all of the water there as highly contaminated.

Sources at the mine say its treatment plants do not have anywhere near the capacity to solve existing water management problems despite recent upgrading of equipment.

For 30 years about 100,000 litres of contaminated water a day has been leaking from the tailings dam into fissures beneath Kakadu but an 18-month review completed last year failed to establish where the water has gone or whether it will damage the environment.

Geoff Kyle, an industrial chemist and science officer working for the Mirarr Aboriginal traditional owners of Kakadu told The Saturday Age that pumping water from the tailings dam was a last resort option for ERA, which it is trying to avoid by asking the mine's regulators to relax environmental standards.

Mr Kyle said the company had proposed ''deliberately allowing seepage into a local aquifer and has submitted detailed plans for remediating the damage it believes will be caused''.

As a water crisis at the long-troubled mine worsened since September, ERA obtained approval from regulators to lift the height of the existing leaking tailings dam by three metres - six metres above its original design height.

The company also obtained permission to allow contaminated water in another disused pit, which is supposed to be undergoing rehabilitation, to rise one metre above a previously approved level.

''They have a pump set up to take 40 megalitres a day from the tailings dam into Pit 3 but we worry it will not be enough,'' said Mr Kyle, a former ERA employee.

''The height limit of the water in the tailings dam is 53 metres - it was 52.9 metres last Friday and there has been more rain since then so we believe the company will have to start pumping if we receive about 100 millimetres more rain.''

The Bureau of Meteorology forecasts unpredictable wet season weather for several weeks.

Since ERA announced an initial three-month suspension of production at Ranger in January, the company's shares have plunged 45 per cent to $6.58 a share - a value loss of $1 billion.

The crisis has thrown into doubt ERA's plans to expand its operation to include an underground mine and the use of a controversial acid heap leach processing technique to process low-grade ore.

Mr Kyle said the Mirarr people who owned the Ranger land took the view that if ERA ''cannot manage what they are already doing, how can they support them doing more?''

ERA chief executive Rob Atkinson confirmed at the company's annual meeting in Darwin on Wednesday that the severe wet weather at the site had raised doubts about whether the company could proceed with acid heap leaching, which has never been tested in a monsoonal climate.

A new report by the Australian Conservation Foundation says ERA has underestimated the size, complexity, cost and impact of the proposed expansion of the mine.

It said acid leaching would pose serious risks to the environment and local indigenous culture as well as complicating ERA's planned closure and exit timeline for the mine, and further increase pressure for an extension to the company's lease beyond its 2021 end date.

ACF campaigner Dave Sweeney said the expansion plan would ''significantly increase contamination loads at Ranger''. ''The company needs to be ending operations and cleaning up, not seeking to expand,'' he said.

The Ranger mine has had more than 150 leaks, spills and mishaps since it opened despite opposition from Kakadu's traditional owners in 1981.

Mirarr senior traditional leader Yvonne Margarula told The Saturday Age last week that her people were ''deeply saddened'' that uranium from their land at Ranger had been exported to Japanese nuclear power companies, including the one operating the stricken Fukushima plant.