Federal Environment Minister Peter Garrett has imposed a ‘controlled action’ order on the proposal, demanding the SA Government prepare an Environmental Impact Statement under the Federal Environmental Protection and Biodiversity Conservation Act.

This means addressing the impact salt water would have on the wetlands’ ecology and on threatened and migratory species, as well as the likely investigation of alternative solutions, such as bio-remediation, that do not require flooding the lakes.

Ashville dairy farmer Clem Mason said he welcomed the announcement by Mr Garrett.

"We are confident that with his understanding of environmental issues that he will see that sea water is an impending disaster that he will not want to sign his name to," he said.

"If salt water gets into Lake Albert it would be irreversible and you’ll get something worse at the southern end of the Coorong.

"It will be dead and an ecological disaster."

Federal Environment Minister Peter Garrett said the EIS would be subject to a "full and rigorous" assessment.

"The South Australian Government’s proposal ... is to be a matter of comprehensive environmental assessment under the relevant Commonwealth legislation and there will be sufficient opportunity for the public to comment on that proposal and any likely decision is still some way down the track," he said.

But Federal Greens Senator Sarah Hanson-Young said the announ-cement was "another nail in the coffin for SA’s Lower Lakes".

"With no announcement of a commitment to finding a non-saltwater option, it seems the Government is simply flying the white flag, and doing little to nothing to avoid what they admit is the worst case scenario," she said.

"Our Lower Lakes must remain fresh."

Making a rare statement on the issue, South Australian Premier Mike Rann reiterated that letting salt water into the Lower Lakes was a last resort measure.

"The Government will leave no stone unturned in investigating all other possible options - such as bio-remediation of affected areas and the use of lime - to protect the lakes from acidification," he said.

"The last thing the Government wants to do is flood the lower lakes with sea water."

There will be a public comment period of 20 business days once the EIS is released.

The EIS will then be updated and Environment Minister Peter Garrett will have 40 days to make a final decision.

The full process is expected to take about three months.