The Murray-Darling Basin Authority has been accused of maladministration, deliberately ignoring the best science on the river, leaning on the CSIRO to alter reports on the adequacy of the basin plan and ignoring the impact of climate change in its future planning.

In a scathing assessment of the authority, counsel assisting the South Australian Murray-Darling royal commission, Richard Beasley SC, has painted a picture of an organisation cowed by its political masters and too afraid to present its own scientific data to the greater scientific community.

“The implementation of the basin plan has been marred by maladministration and mismanagement,” Beasley said. “Responsibility for that falls on current executives and the board.”

Beasley has highlighted serious allegations about the adequacy of the MDBA’s modelling which came up with the figure of 2,750 gigalitres of water to be recovered for the environment under the plan. Numerous scientists regarded the number as too low.

This recovery target is central to the plan and is now being cut further as a result of amendments which aim to achieve the same environmental outcomes without having to buy water from farmers.

“Most scientists – no, every scientist – who gave evidence described the setting of the sustainable diversion limit [SDL, the amount to be recovered] and the environmentally sustainable level of take [ESLT, the amount that could be safely extracted from the river system] as ‘not science’.”

Commissioner Bret Walker (left) listens to Richard Beasley SC at the royal commission in Adelaide on Tuesday. Photograph: James Elsby/AAP

He said that scientists had accused the MDBA of keeping its modelling on this crucial target secret and refusing to have its science peer reviewed or its modelling tested.

Beasley said one retired MDBA staff member, the former head of environmental water David Bell, had referred to jokes inside the authority about the recovery target as being linked to Barnaby Joyce’s postcode, and that “everyone understood the figure had to start with a 2,” he said.

Dr Matthew Colloff, a former CSIRO scientist, described the 2,750 figure as “not being science” while Professor John Williams described it as a “muddle and not defensible”, Beasley said. The Wentworth group of concerned scientists had given evidence that there was nothing from a scientific point of view that justified the 2,750GL figure.

Colloff, who retired in 2016 also gave evidence that that his draft report on a 2,800GL plan had been altered by CSIRO management in a way that was “misleading and amounted to scientific censorship”.

The draft had concluded that the plan would deliver only 55% of the environmental water needs, but this was not what the MDBA wanted to hear, Beasley said.

Colloff had kept a draft of his report and notes, and that at one stage mediators were brought in to the CSIRO to try and smooth over the outcry among staff, he said.

“It happened. That conduct cannot be swept under the carpet,” he said.

Beasley also highlighted the fact that the MDBA had not included the impact of climate change in the basin plan.

He referred to evidence by Professor Andy Pitman from the University of NSW and others that it is getting hotter in the basin and that hotter periods would last longer. Pittman warned that climate change can happen very rapidly and abruptly and that it should have been factored in since the start of the plan.

Beasley also accused the authority of acting unlawfully under its own act – the Water Act 2007 – and of deliberately taking into account factors that political masters of both stripes urged upon it.

“There is no triple bottom line in the act,” he said referring to the common claim by both the federal government and the Murray Darling Basin Authority that it must consider environmental, social and economic impacts when setting the amount of water to be recovered for the environment.

“That is a public relations soundbite, made up by the authority perhaps because its what they think people want to hear,” he said.

The Water Act was an environmental statute, that gained its validity due to the treaties Australia had signed such as the Ramsar treaty to protect wetlands, Beasley said.

“It’s nauseating to me to hear this so called triple bottom line,” he said “There is no trade-off between the environment on one hand and economic outcomes on the other.”

The federal government refused to allow its bureaucrats to participate in the South Australian royal commission, and launched a high court challenge to subpoenas that were issued to try to compel evidence from the MDBA.

The commissioner, Bret Walker SC, backed off after the newly elected Liberal state government refused to extend his reporting date, saying he did not have sufficient time to provide procedural fairness, if he won the high court tussle.

If Walker agrees with the assessment of his counsel assisting, the Murray Darling Basin plan is now almost certainly facing challenge to its validity.

There have been questions about whether a state-based royal commission will have much impact on a government which is now in the throes of implementing further adjustments to the basin plan, which will further take the pressure of buybacks of water from farmers.

But this is the second major alarm to be sounded about whether the plan is failing.

In August the Productivity Commission warned the Murray-Darling Basin plan could fail to deliver on its next phase and $5bn of taxpayers’ funds is at risk unless urgent changes are made.

The final productivity commission report is due in December. The South Australian royal commission is due to report by February.