The Morrison government and its bureaucrats are under the microscope over the 2015 purchase of water from two Queensland properties owned by Eastern Australia Agriculture under the Murray Darling Basin Plan.

It has since emerged that a parent company, Eastern Australia Irrigation, was domiciled in the Cayman Islands, a known tax haven. Energy Minister Angus Taylor co-founded the parent company and directed it until he was elected to Parliament in 2013, but denies benefiting from the transaction.

Critics say the deal was poor value for money and will deliver few environmental benefits.

Mr Joyce, who signed off on the deal, says he relied on expert advice from his department and that the Queensland Labor government had pushed for the purchase.

In a heated interview on ABC Radio on Monday night, Mr Joyce said unless the Queensland government were "morons" or "asleep", he assumed their 2015 proposal meant the deal he signed was sound.

In November 2015, the Queensland Labor government's Minister for State Development, Natural Resources and Mines, Anthony Lynham, proposed that the federal government buy water entitlements from Eastern Australia Agriculture.

However Dr Lynham on Tuesday said the deal he proposed was vastly different to the one signed off by Mr Joyce two years later.

Dr Lynham had suggested the Commonwealth buy the two cotton properties in their entirety, including almost 56,000 megalitres of water entitlements, infrastructure and the farm enterprises. He said a desktop assessment by his government suggested the assets were worth $123 million.

Under the deal signed by Mr Joyce, the Commonwealth received about 29,000 gigalitres of overland water flows - available only after rare flood events - for $79 million. This deal did not involve buying the farms or associated infrastructure.

Dr Lynham told ABC Radio that Queensland's proposal was "very, very different" to the one Mr Joyce agreed to. He said Mr Joyce, as the federal minister, was also responsible for conducting due diligence on the deal and ensuring the price was fair, adding the Queensland's role was "administrative" and involved only the transfer of water rights.

He said while the 2015 proposal was "a good deal for Queensland" but that the federal government abandoned discussions around the time Mr Joyce took the water portfolio.

"It was a wasted opportunity ... It was Barnaby Joyce's decision to subsequently buy the unreliable overland flow of 28,000 megalitres in 2017 and it was his decision to pay $80 million," Dr Lynham said.

"There are some serious questions to be answered by Barnaby Joyce here."

Meanwhile, the Morrison government has asked the Auditor-General to examine a decade's worth of water buybacks amid sustained pressure on the Coalition over a $79 million deal with a Cayman Islands-linked company.

Agriculture Minister David Littleproud has requested the Auditor-General review "to make sure the community can continue to have confidence in the Murray-Darling Basin Plan".

The review would involve all water purchases since 2008, including under the former Labor government.

The Morrison government and its bureaucrats are under the microscope over the 2015 purchase of water from two Queensland properties owned by Eastern Australia Agriculture. Such deals are a central features of the Murray Darling Basin Plan, which seeks to recover water from irrigators and return it to the environment.

Network Ten's The Project last week reported that at the time of the deal, Eastern Australia Agriculture was owned by a parent company, Eastern Australia Irrigation, which is based in the Cayman Islands - a known tax haven. Angus Taylor, now the Energy Minister, co-founded the parent company and was a director until he entered Parliament in 2013.

Mr Littleproud said he has "confidence all things from all parties were done properly" in relation to the deal, and the review would "make sure all governments of all political persuasions since 2008 have done the right thing".

Mr Littleproud said he didn't "see any evidence to support a royal commission" - a move that Labor has not ruled out if it wins office in May.

"If you do not rely on the competent advice from the department, who on Earth are you going to rely on?" he asked, describing Labor's criticism as "a load of horse crap".

Labor leader Bill Shorten on Tuesday ramped up the party's rhetoric on the need for a federal royal commission into the basin plan, questioning why Prime Minister Scott Morrison was "not launching a judicial inquiry into the growing scandal" around the Eastern Australia Agriculture deal.

"Every day goes by, the suspicions grow. It won't be good enough if you have a tick box review, Mr Morrison," the Opposition Leader said.

Mr Shorten said a judicial inquiry would have the power to compel witnesses and "get to the bottom" of questions over the arrangement.

- SMH/The Age