Queensland farmers have highlighted what they say is another failure of the Murray Darling Basin Plan.

Farmers on the McIntyre River say cotton irrigators have been selling water back to the Commonwealth, and then replacing it for free with extra floodwaters caught off nearby plains.

They say water is getting backed up high in the system, effectively wasting millions of taxpayer dollars spent on local water efficiency projects with no actual water savings achieved.

The farmers have told reporters that the Murray Darling Basin Authority (MDBA) classifies the overland floodwater that ends up in dams as ‘leakage’ and does not count it in its administration of the Basin Plan.

Bill Johnson, the former director of environmental water planning for the MDBA has told the ABC that the national plan to return water to the river system had only perverse outcomes.

“In my view it's extremely serious,” he said.

“It couldn't be more serious. The Government has invested about $13 billion aside for this and it seems as though it isn't getting good value for money.

“In some parts I think the outcomes are perverse. The outcomes are possibly the opposite of what was intended.”

It is just the latest report on potentially large gaps in the running of the $13 billion Basin Plan, and has prompted South Australian senator Nick Xenophon to again call for a royal commission.

“It looks like this $13 billion project, this nation-building plan to save the river, to save farming communities is being built on a house of cards because the compliance mechanisms just have so many holes in them,” he said.

Senator Xenophon said Deputy Prime Minister Barnaby Joyce had lost his credibility as minister for water and agriculture by failing to juggle the competing interests of the two portfolios.