The federal government has refused to release advice which it says shows the Murray-Darling Basin Plan is in line with commonwealth law.

Despite scathing findings from the South Australian royal commission questioning the legality of the plan, the Murray-Darling Basin Authority is urging federal and state governments to remain faithful to it.

The inquiry found the Water Act had been breached, but the government denies that, based on legal advice.

Assistant Water Minister Richard Colbeck told Senate estimates on Friday the government was following longstanding practice to not release sensitive legal advice.

Greens senator Sarah Hanson-Young and fellow South Australian Rex Patrick accused the government of withholding important information from the public.

They both want the plan to be overhauled, pointing to the royal commission as evidence it has failed.

"This is a train smash. If you can see the train about to go off the track then you can stop it," Senator Patrick said.

Murray-Darling Basin Authority chief executive Phillip Glyde said the best way to return water to the environment and improve efficiency in irrigation was to stay the course with the 12-year plan.

"There's been a train crash in relation to the Murray-Darling Basin for 50 years or more. There is a solution in place," Mr Glyde said.

Senator Colbeck warned major changes would destroy the political consensus it was built on, undermining its aims.

While commissioner Bret Walker found there had been serious maladministration by the MDBA, Mr Glyde said they couldn't find any evidence in the report to back up the claim.

The government is also weighing up the Productivity Commission's recommendation it be split into two bodies, a management body and a regulator.

MDBA compliance officer executive directors Russell James said the perceived conflict was overstated.

"There is a view in some of the reports that the authority is marking its own homework. I don't think that assessment is correct," Mr James said.