A scathing report examining the Murray Darling Basin Plan has reignited debate over how to manage the waterways, with some warning the proposed changes could shut down regional towns.

Key points: Victoria's Water Minister said up to 12 regional towns would not survive if more water was reserved for the environment, as recommended

Victoria's Water Minister said up to 12 regional towns would not survive if more water was reserved for the environment, as recommended Some scientists want an overhaul of the basin plan and said without it small towns could lose drinking water

Some scientists want an overhaul of the basin plan and said without it small towns could lose drinking water Greens Senator Sarah Hanson Young has called the report damming and said chief executive Phillip Glyde should resign

The South Australian Royal Commission into the Basin Plan made 44 recommendations and called for a major overhaul to the management of the waterways.

Commissioner Bret Walker SC said more water should be reallocated from irrigation to the environment, but the Victorian Water Minister Lisa Neville said that was a bad idea.

"I think at this point to change the goal posts, to move away from this, would be in my view disastrous," she told AM.

Ms Neville said Victorians would be forced to find new homes if more water was allocated to the environment, because up to 12 towns would "not survive".

"Townships like Shepparton, Swan Hill and others have already seen job losses in the vicinity of 40 per cent, largely as a result of reducing water availability for production," she said.

Scientists and politicians are split on the recommendations from the Murray Darling plan. ( Supplied: Mark Moxham )

However, a number of scientists do not agree, including Jamie Pittock from the Wentworth Group of Concerned Scientists, who said an overhaul of the basin plan is needed.

"We've been concerned for some time that many of the key measures in the basin plan aren't based on rigorous science and we are welcoming the royal commission's findings that a number of major changes are needed to ensure the basin plan delivers the $13 billion worth of work that the public expects," he said.

Professor Pittock said the environment and people living in regional centres would suffer if state and federal governments do not accept the recommendations.

"We will see increasing blue green algae blooms, fish kills, death of flood plain forests, we will see small towns losing their access to drinkable water, we will see pastoralists being forced to shut down their operations because their livestock won't have safe water to drink and the tourism industry will suffer," he said.

Politicians want further action following report

The royal commission report was scathing of the Murray Darling Basin Authority (MDBA) and Commissioner Walker found Commonwealth officials acted unlawfully and were grossly negligent.

Shadow Environment Minister Tony Burke said he was alarmed by the findings and wanted to know more details about the behaviour described in the report.

"We are calling for the findings that have been made in the royal commission to be referred to the Australian Public Service Commissioner so there can be a proper investigation," he said.

"If these findings are right then serious action needs to be taken by the Commonwealth and if those findings are based on the fact that not all the evidence was before the commission then those people need to have their names cleared."

Greens Senator Sarah Hanson-Young said the report was damning and called for the authority's chief executive Phillip Glyde to resign.

"It's time for him to step down, for a new head to be put in place, someone who can restore confidence and put the environment back at the centre of the process of saving the river," she said.

The MDBA issued a statement that rejected the assertion by the Commission that it acted improperly or unlawfully in anyway.

"The MDBA is confident that the Basin Plan has been made lawfully and is based on best available science. There is extensive documentation in our published reports to support this," the statement said.