Deputy Prime Minister Barnaby Joyce has accused the ABC's Four Corners program of taking part in a campaign to take more water away from irrigators, which would shut down towns.

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At a Pollies in the Pub event, Mr Joyce last night told a crowd gathered at a hotel in Shepparton, Victoria, that the program's investigation was trying to create "a calamity".

"A calamity for which the solution is trying to take more water off you, shut more of your towns down," Mr Joyce said.

Mr Joyce was responding to allegations raised in the program that some New South Wales cotton farmers were stealing water.

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Earlier in the day he had told Canberra reporters the program raised serious concerns about water theft.

But to the river community, he was using different language.

"I'm glad it's our portfolio, a National Party portfolio because we can go out and say no, we're not going to follow on that, we're not going to scare you," he said.

"We've taken water, put it back into agriculture, so we can look after you and make sure we don't have the greenies running the show."

'He's been deeply two-faced'

South Australian Water Minister Ian Hunter said he had long believed Mr Joyce was not committed to the Murray-Darling Basin Plan.

Ian Hunter wants a judicial inquiry into NSW's Murray-Darling Basin Plan's water management. ( ABC News )

"He really is telling people what he really thinks and the Deputy Prime Minister responsible for delivering the Murray-Darling Basin Plan is actually telling people he's going to undermine it," Mr Hunter said.

"There's a deep suspicion that he's been deeply two-faced on this matter.

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"Telling one story to one group of people somewhere on the river and another story elsewhere."

South Australian senator Nick Xenophon labelled the comments incredible foolish, saying the water portfolio should be split from agriculture.

"It can lead to potential and real conflicts of interest and that is why the portfolio must be split," Senator Xenophon said.

"The environment portfolio should be covering water and not agriculture.

"Blaming Four Corners for the problems in the Murray-Darling Basin is a bit like blaming Nero's fiddle for the fires of Rome."