Federal and state politicians are demanding an independent inquiry into allegations that billions of litres of water purchased by the taxpayer to help save the Murray River was instead harvested for use by cotton farmers.

South Australian federal senator Nick Xenophon and SA state water minister Ian Hunter on Tuesday called for the allegations to be investigated by a judicial inquiry, which would have the same powers as a royal commission.

The allegations, aired by the ABC’s Four Corners program, included claims that water earmarked for environmental use had been instead used by NSW cotton farmers and that a top NSW water official had offered to share confidential information with irrigation lobbyists.

Federal Labor water spokesman Tony Burke said an “urgent overview” promised by the NSW government was insufficient.

Mr Burke said he had asked the Australian National Audit Office to investigate.

“There’s no doubt there are some people within the NSW government who are trying to undermine the plan,” he said.

“There’s no doubt there are some people within the NSW government who have no respect for the health of the river,” .

Mr Burke, who signed off on the Murray-Darling Basin plan as water minister at the time, also claimed that Deputy PM and Water Resources Minister Barnaby Joyce had “gone missing”.

Environmental water has been set aside to help save the Murray. Photo: Getty

Mr Joyce is yet to respond to the Four Corners story, but has said the issue is a state matter.

He did not respond to a request for comment from The New Daily.

Assistant Water Resources Minister Anne Ruston said there were “serious questions” for the NSW government to answer, describing the allegations as “hideous”.

“I certainly think it’s a serious wake-up call if somebody is actually stealing water,” Senator Ruston told the ABC.

“That’s a serious allegation and we need to find out if it is true.”

On Monday, Four Corners reported that in the Barwon-Darling area, billions of litres of environment water purchased by the government through the $13 billion Murray-Darling Basin plan was instead being pumped into storages to grow cotton.

The program also aired a recording in which top NSW water bureaucrat Gavin Hanlon appeared to offer to share confidential information with irrigation lobbyists.

Greens senator Sarah Hanson-Young said she would push for a Senate inquiry when Parliament returns in two weeks.

“The revelations of stealing of water, tampering with meters in New South Wales, are extraordinary and they must be investigated fully, frankly and urgently,” she said.

“The Senate has the power to give whistleblowers parliamentary privilege so that they can speak freely about the information they have.

“I think we have to leave no stone unturned here.”

NSW Water Minister Niall Blair said on Tuesday that the NSW Department of Industry would provide an “urgent overview of all the compliance matters raised in the program”.

“The NSW government remains committed to the Murray Darling Basin Plan, while seeking the best deal for NSW communities within that framework,” he said in a statement.

He had also asked for “clarification” around the briefings given by Mr Hanlon.

The Murray-Darling Basin plan was created to ensure water was “shared between all users, including the environment, in a sustainable way”, according to the government.