The Federal Agriculture Department is standing by a controversial water buyback deal worth tens of millions of dollars, which Labor says is a "scandal" worthy of inquiry.

Key points: The company at the centre of the buybacks was once associated with Energy Minister Angus Taylor

The company at the centre of the buybacks was once associated with Energy Minister Angus Taylor In 2017, water licences were bought from two Queensland properties owned by that company, for $80m

In 2017, water licences were bought from two Queensland properties owned by that company, for $80m Mr Taylor and Mr Joyce have both released statements clarifying their roles

The questions surrounding the involvement of Nationals MP Barnaby Joyce and Energy Minister Angus Taylor in $80 million of water buybacks has resurfaced as an election campaign issue, with Labor leader Bill Shorten declaring there are "probity questions as far as the eye can see".

In 2017, taxpayers' money was used to purchase water licences from two Queensland properties owned by Eastern Australia Agriculture (EAA), a company Mr Taylor was once director of but never had a financial interest in.

The deal was signed off by then-agriculture minister Barnaby Joyce, even though it had previously been rejected twice.

EAA is controlled by Eastern Australia Irrigation, which is based in the Cayman Islands, and that is where some of the proceeds from the sale ended up, according to a report by Network Ten's The Project.

The deal is part of a series of controversial agreements amounting to a total of $200 million, which used funds allocated for purchasing environmental water under the Murray-Darling Basin Plan.

They occurred without an open tender process.

In a statement, Mr Taylor said he "concluded all association with EAA and related companies prior to entering the Parliament" and that he had "no knowledge of the Federal Government's water buyback from EAA until after it occurred".

He also said he had never had a direct or indirect financial interest in EAA, or any associated company.

But questions remain about the purchase, including whether the deal represented value for money to taxpayers.

PM Scott Morrison (pictured with Angus Taylor) said the issue had been raised, examined and addressed. ( ABC News: Nick Haggarty )

In a statement, a spokesman for Mr Joyce said the former agriculture minister had no role in determining either the price of the deal, or the vendor.

"They were done at arm's length by the Murray-Darling Basin Authority in conjunction with the Commonwealth Environmental Water Holder," the statement read.

'Probity questions as far as eye can see': Labor

Labor leader Bill Shorten said the deal had raised many questions.

"This water scandal is really, really, starting to come to light," he said.

A spokesman for former agriculture minister Barnaby Joyce said the deal was "done at arm's length". ( ABC News: Adam Kennedy )

"This was the nation's biggest water purchase, the most expensive water purchase, and now you're seeing questions about the probity of it.

"You've got the particular minister, Mr Taylor, he used to make a living from working with this company, [he] goes into Parliament, and then the company gets a super contract.

"[There are a] lot more questions to answer here … Probity questions as far as the eye can see."

He called on Prime Minister Scott Morrison to conduct an audit into the issue.

"The Prime Minister needs to say [if he is] completely confident that everything is above board. Is he going to stake his reputation on whether or not all these matters have been above board?" Mr Shorten said.

"If he is, will he agree to an audit or commission of inquiry to demonstrate the questions that have been raised are not valid?"

Deal presented 'unique opportunity': Department

As Mr Morrison prepared to front reporters in Sydney, the Department of Agriculture sent out a statement defending the decision.

It said the purchase presented a "unique opportunity" to secure almost 30 gigalitres of water in a catchment of strategic importance.

It also rejected reports the water was worthless and could not be used.

"The water has clear and very significant environmental benefits for the Lower Balonne, including the Culgoa and the Narran Lakes — a Ramsar-listed wetland of international importance," the statement read.

Mr Morrison said proper process was followed.

"The Senate has actually inquired into this matter and sought production of documents from the Government regarding those transactions, which the Government has provided," he said.

"There's a high level of transparency on that.

"This is an issue that has been raised before, and has been addressed."