Deputy Prime Minister Barnaby Joyce has stoked the controversy over claims of water theft in NSW aired by the ABC, dismissing the report as a ploy to strip more water off rural communities.

The comments have prompted the South Australian government to call for his removal from the post of federal water minister.

Mr Joyce told a gathering in a pub on Wednes

day evening in the northern Victorian town of Shepparton, that it was important the Nationals had taken control of the Murray Darling Basin Plan.

"[We've got] $13 billion invested in it," Mr Joyce said, referring to the plan, according to a recording by the ABC. "We've taken water and put it back into agriculture [ministry] so we can look after you and make sure we don't have the greenies running the show, basically sending you out the back door."

Mr Joyce took aim at the Four Corners investigation broadcast this week that identified apparent rorting by some irrigators of billions of litres in the Barwon-Darling region of northern NSW.

The program stirred national concern and prompted NSW water minister Niall Blair on Wednesday to appoint a former head of the National Water Commission Ken Matthews to conduct an independent probe of the claims.  

Mr Joyce downplayed the impact of the alleged water theft at a media conference in Canberra on Wednesday - likening it cattle rustling - before dismissing the claims further at the Shepparton gathering.

"You know what's [the Four Corners program is] all about - it's about them trying to take water off you, [to] paint a calamity," he said, according to the recording. "A calamity, for which the solution is that they're going take more water off you, and shut more of your towns down."

'Doesn't get it'

A spokesman for Mr Joyce said the deputy PM said Mr Joyce's comments were directed at "those people, including radical greens, who want to throw the Murray Darling Basin Plan out the door; and who want to engage in failed water buy backs".

Mr Joyce said by earlier comments that any alleged rule breaking must be promptly investigated and appropriately dealt with. "The vast majority of the irrigation industry follow the rules and the government stands by them,' the spokesman said.

But Tony Burke, Labor's environment spokesman, said it was "day four [after the program] and Barnaby Joyce still doesn't get it". 

"This isn't some sort of National Party game. The allegations are about theft, corruption and a small number of very big irrigators ripping everyone off," Mr Burke said.

"As minister for water, it's Barnaby Joyce's job to be defending the entire basin, not making light of allegations that may well be criminal."

'Opposite' view

Ian Hunter, the South Australian water minister who has clashed with Mr Joyce in the past, said Mr Joyce had been caught telling the national media one thing in Canberra and "completely the opposite" in a pub.

"The minister in charge of putting 3200 gigalitres of water back into the Murray is telling people in pubs that instead he will put it back into agriculture," Mr Hunter said.

"He is incapable of delivering the Basin Plan and the Prime Minister must now remove that portfolio from him," he said.

Environmental groups have been concerned that the water portfolio grabbed by Mr Joyce when Malcolm Turnbull ousted Tony Abbott as Prime Minister had transferred Nationals critical control of a key environment asset. NSW water minister is also a Nationals MP in the Berejiklian government.

"I'm glad that [water's] in our portfolio, the Nationals Party portfolio, because we can go out and say 'no, we not going to fold on that, we're not going to scare you'," Mr Joyce said in Shepparton. "Our focus is to ensure your economic fortunes are advanced from what we do."

Mr Hunter also renewed his call for a judicial inquiry into the claims made by the Four Corners report, saying the NSW inquiry's terms of reference were too narrow. Any serious investigation needed to have powers to demand documents and for individuals to appear in person.

A spokeswoman for Mr Blair said Mr Matthews would be able to investigate all issues raised by the program and identify if further investigations are required.

The spokeswoman also defended Mr Matthews record of involvement in the water industry since retiring from the now-defunct National Water Commission in 2010.

"The only potentially relevant work undertaken by Mr Matthews since his retirement from the National Water Commission is his role as director and more recently, chair of the board, of Waterfind Holdings - a South Australian based water broking company," the spokeswoman said, adding that Mr Matthews resigned from that role on 23 June 2017.