A scathing report into Australia’s Murray-Darling Basin Authority has found it acted unlawfully and called for water allocations to be completely overhauled.

The royal commission report, released on Thursday, found river allotments in the multibillion-dollar deal across Australia’s largest river system were driven by politics.

It accused the basin authority board of maladministration with its disregard for science. The report said water levels must be made on a scientific basis and in accordance with reconstructed water laws.

The South Australian inquiry also called for uniform penalties between basin states for irrigators who don’t comply with regulations.

Commissioner Bret Walker SC’s 736-page final report includes 111 findings and 44 recommendations aimed at improving the effectiveness of the Murray-Darling Basin Plan.

Prominent among them are its finding that the Murray-Darling Basin Authority acted unlawfully when it “completely ignored” climate change projections for the determination of water allocations.

“The [sustainable diversion limit] ignores the best available scientific knowledge,” it said.

“As an administrative decision, it is indefensible.”

The 12-month investigation into the Murray-Darling Basin Plan was prompted by allegations of water theft by NSW cotton farmers. Those claims have been renewed in the wake of three mass fish deaths in the Darling River in recent weeks.

Locals in the outback town of Menindee have blamed the deaths on water use by cotton irrigators, as well as authorities’ decisions to empty the Menindee Lakes in 2014 and 2017.

Cotton Australia has denied the allegations.

The 2012 Murray-Darling plan recommended resetting water-saving limits, repealing the outcome of the Northern Basin Review and new measurements for water on floodplains. It aimed to return 2750 gigalitres of water to the basin system to help the environment.

But Mr Walker said the basin authority had failed to implement the changes.

“Regrettably, from prior to the time of the enactment of the basin plan, the MDBA has shown itself to be unwilling or incapable of acting lawfully,” his report found.

On Thursday, South Australian Premier Steven Marshall said the royal commission had strayed from its initial aim.

The Liberal leader vowed to look at the legality of the plan and respond later in the year.

Mr Marshall will ask Prime Minister Scott Morrison to convene a meeting of the Murray-Darling basin states to look at the inquiry findings.

“I don’t want to be drawn on providing commentary at this early stage,” he said.

“But I can assure every single person in this state, we are taking this royal commission report extraordinarily seriously.”

He said the inquiry had not focused on allegations of water theft in the basin, despite his Labor predecessor promising it would.

The royal commission also criticised the actions of SA Water Minister David Spiers, saying they were a “capitulation” to the Commonwealth and contrary to South Australian interests. Mr Spiers rejected that.

“It is an isolated comment that doesn’t consider all the other things that occurred,” he said.

He said the government had got 450 gigalitres for the environment and $70 million for the Coorong, at the ocean end of the Murray River.

-with AAP