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"That’s the shocking thing for me - that there’s insufficient environmental water upstream to maintain the basic health of the river in dry times," he said.

The report was compiled by leading scientists chosen by the academy and shared findings with those working on a separate study led by former Bureau of Meteorology head Rob Vertessy and commissioned by the Morrison government. The Vertessy report is expected to be released this week.

Labor is still considering the report's findings, after receiving it last night.

"The Murray Darling Basin Plan was well designed by Labor, but its implementation has been mismanaged by the Liberals," Mr Shorten said. "That’s hurting the river, hurting farmers and hurting the environment."

Labor's water spokesman Tony Burke called for an urgent meeting of water ministers in the basin states with the Commonwealth government and the Murray-Darling Basin Authority to establish how environmental flows can be secured.

Mr Burke said it was clear the science underpinning the sustainable diversion limits needed to be updated. If that review showed the northern basin review savings needed to changed, "it lands where it lands", he said, suggesting Labor would be open to a revision.

The Academy report also backed other Labor positions, including a removal on the limit placed by the federal Coalition government on buybacks of water from farmers, he noted.

'Urgent steps'

The three big fish kills, beginning in mid-December last year, have been blamed on blue-green algal blooms amid stagnant flows and heatwaves.

Changing weather conditions killed some of the algae that, in turn, depleted dissolved oxygen levels to below the survival point for Murray cod, perch, bony herring and other species.

The academy's study calls for "urgent steps" to be taken within six months to ensure sufficient flows to prevent further fish kills, including the creation of a Menindee Lakes restoration project.

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Professor Moritz said upstream water diversions had contributed to the lack of water reaching the lower Darling River but how much was unclear because of the absence of data.

He said accounting of water use was "particularly poor" for the northern basin.

"The [Murray-Darling Basin Authority] estimates they are catching only between a quarter and a half of the water extraction, and it's more like 80-90 per cent in the southern basin," Professor Moritz said.

Climate change, though, posed different issues for the regions. The southern basin's projections point to a clearer drying trend but "are quite uncertain for the northern basin", he said.

The study recommended the governments revisit its plans for a so-called Sustainable Diversion Limit project for Menindee Lakes that would reduce their storage capacity in a bid to cut evaporation losses.

Instead, "we suggest that the system be managed to maintain at least 400 [billion litres] of accessible water" in the lakes, the report said.

"This more ecologically sustainable approach would not deliver as much water savings, but would improve environmental outcomes under the Murray-Darling Basin Plan, specifically targeting the range of different organisms and ecological processes, including conservation of habitat for native fish species and waterbirds, including migratory shore birds," it said.

"We need to be rethinking how we consume this incredibly important asset," Professor Moritz said.

'Contradictions'

Niall Blair, NSW's Minister for Regional Water, said the report appeared to have "some contradictions".

"On the one hand, it debates the environmental outcomes that could be achieved by releasing the available water down the Darling, citing water quality concerns and concerns around the amount of water, yet then recommends that this water is released within six months, regardless of whether rainfall has occurred in the northern catchment," Mr Blair said.

"There are also findings that we directly disagree with, namely that the cap on buybacks should be lifted as well as the assertion that the Northern Basin review should be repealed," he said.

David Littleproud, the federal Agriculture Minister, said the report was "deeply disappointing" to have Labor "politicise the issue by commissioning an organisation which has Bill Shorten’s former key staff member [as chair]".

“The recommendation to scrap the 1500-gigalitre cap on water buybacks is purely political," he said. "Scientists should not be concerned about how water is recovered; only how much of it goes down the system, when, and what environmental outcomes that produces."

“Taking ‘urgent steps to ensure there is sufficient flow’ in the Darling is impossible unless these scientists know a really good rain dance," Mr Littleproud said.

The Greens, though, said the Academy of Science report reinforced to need for a federal Royal Commission "to clean out the corruption, maladministration and incompetence".

“This report highlights the limitations of environmental water accounting and the grave danger posed by water use including floodplain harvesting and theft of overland flows, particularly in the northern basin," Senator Sarah Hanson-Young, the Greens water spokeswoman, said.