The Federal Government has ordered an interstate review of water use in the Murray-Darling Basin, a week after serious allegations surrounding compliance were aired by the ABC's Four Corners program.

The Commonwealth initially refused to investigate the alleged cases of water theft in New South Wales, putting responsibility back on state governments.

But Federal Water Minister Barnaby Joyce will now write to ministers in Basin states, asking for their agreement to an independent compliance review.

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A joint statement released by Mr Joyce and Prime Minister Malcolm Turnbull said the review would be run by the Murray-Darling Basin Authority (MDBA) and investigate if there had been any breaches of state laws governing water use.

"We expect that, as part of their agreement to the review, Basin water ministers will commit to providing the MDBA with ready access to all relevant information and the full support and cooperation of relevant state officials," it said.

The Four Corners program highlighted alleged cases of "water theft" by some farmers in the Barwon-Darling valley, claiming they had taken more water from the river than they were entitled to.

It also revealed meters had been tampered with, masking the amount of water pumped into some farm dams in the region.

At the time, Mr Joyce refused calls for the Commonwealth to step in and investigate, and said "the issue is overwhelmingly an issue for New South Wales".

He also accused Four Corners of taking part in a campaign to take more water away from irrigators and "create a calamity ... for which the solution is trying to take more water off you, shut more of your towns down".

The review will identify the highest areas of risk of non-compliance and the adequacy of water monitoring arrangements.

It will run alongside several other investigations, including a review by the New South Wales Independent Commission Against Corruption (ICAC).

The MDBA will report back by the end of the year.