A leaked letter suggests South Australia used 45 gigalitres of entitlement water as drinking water, rather than for the environment.

The letter reportedly shows the Commonwealth Environment Water Holder, Mr David Papps, warned SA's water department in December 2015 that diverting the 45 gigalitres created risks for the environment of the Coorong and Lower Lakes.

“My office has asked your department to reconsider plans to defer entitlement flow over the summer months to help increase barrage flows into the Coorong over summer while maintaining minimum lake levels, however these plans remain unchanged,” Mr Papps said.

“I am concerned that South Australia's plan to defer entitlement flow during summer poses additional risks to the Coorong and undermines the effective use of Commonwealth environmental water to achieve agreed objectives under the Water Schedule and the Basin Plan.”

South Australia's water minister Ian Hunter says he rejected the advice, and informed the CEWH it would be using the water as drinking water instead.

“We said; ‘No, critical human water needs planning trumps this’, and that is what the Murray Darling Basin agreement is about, us providing for critical human water needs,” he said.

“It was held back for drinking water, because 90 per cent of South Australians depend on Murray water for drinking purposes.'”

NSW water minister Niall Blair criticised the South Australian Government for not being transparent enough with its water-use.

“This [letter] raises the question about the South Australian Government's commitment to the environmental objectives set out in the basin plan. The public deserves an explanation,” he told News Corp reporters.

South Australia’s yearly entitlement is 1850 gigalitres.

Of that amounts, 696GL disappears through dilution, and 876GL goes to irrigators for farming, SA Water or for the environment.

Mr Hunter said the remaining 278 GL is for future water needs, including drinking water.

“We have never actually deferred the full amount, the highest we have ever deferred is 160GL, so we have drinking water for the state,” he said.

“This is misinformation out of NSW, who are desperate to cover up the wrongdoings in that state, by trying to look at some letter from the Commonwealth to pin us.”

Mr Hunter said it is more evidence of the need for a royal commission into Murray-Darling water use.

“There is something crook in NSW and we all know about it, this is why we need to have a Commonwealth led royal commission to get to the bottom of it,” he said.

“If they have allegations to raise about SA's application of the rules, let them bring it to a royal commission, what have they got to hide, because we have nothing to hide.”

Steve Whan from the National Irrigators Council said political bickering did nothing to help the basin plan.

“We have seen people quick to accuse other states of not supporting the plan, but what this shows is allegations go both ways and that we all need to take constructive approaches,” he told the ABC.

“The basin plan is a compel instrument and will take a fair bit of time to implement and gained everyone's trust.

“I would like to see the political point scoring come out of the entire basin plan process, which means the ministers continue to work constructively like they were at the beginning of the year.”