Labor will seek an inquiry with coercive powers into taxpayer-funded water buybacks after a government department failed to meet a deadline for documents.

Agriculture Minister David Littleproud has asked the auditor-general to look into the controversial $80 million purchase, as well as other purchases dating back to 2008.

But Labor frontbencher Tony Burke said the Agriculture Department's failure to provide documents by close of business on Tuesday was "not acceptable" and it was now clear an independent inquiry into the Eastern Australia Agriculture water buyback was needed.

"The government's chaos has meant the documents the Labor party sought by close of business have not been received," Mr Burke said in a statement on Tuesday night.

"Scott Morrison is trying to cover up his government's incompetence, chaos and potential misconduct."

The department declined to comment beyond its statement issued last week that the purchase was in line with procurement rules and paid at a "fair market rate".

Mr Littleproud wrote to the auditor-general Grant Hehir on Tuesday asking him to look at water buybacks over the past decade to provide confidence to the community.

Questions have re-emerged during the election campaign about a buyback of 28.7 gigalitres of water from two Eastern Australia Agriculture-owned Queensland properties, Clyde and Kia Ora, for $78.9 million.

Labor leader Bill Shorten earlier said the department needed to provide unedited documents about the buyback by 5pm.

"Not with a big texta marking out all the interesting details but the fair dinkum paperwork, without the redactions, without the secret squirrel business which this government loves," he said.

Shadow treasurer Chris Bowen described the auditor-general review as a "cute little trick" to ward off unanswered questions.

Mr Morrison insists the water buyback program has been run strictly within the rules and subject to regular reviews by the auditor-general.

The prime minister dismissed suggestions there was anything wrong with Eastern Australia Agriculture donating $55,000 to the Liberal Party four years before the sale.

The Greens have pushed for a royal commission into the Murray-Darling Basin Plan over the water buyback.

But the government has rebuffed those calls, arguing there is not enough evidence to necessitate a costly inquiry.

Mr Morrison is confident Barnaby Joyce, who was minister responsible for water at the time, acted appropriately despite questions over the high price and the company's links.

Mr Joyce is "100 per cent" confident the auditor-general will clear him of any wrongdoing, saying he had nothing to do with selecting the buyer or setting the price.

"I'm absolutely confident we have done absolutely nothing wrong," he told reporters in Tamworth.

Mr Morrison noted the previous Labor government had dealt with Eastern Australia Agriculture, citing a separate $300 million water purchase.

Labor argues the difference is that its buybacks were conducted through a competitive tender process.

Mr Morrison has also defended Energy Minister Angus Taylor, who was once a director of Eastern Australia Agriculture.

Mr Taylor co-founded the company that sold the water, but said he'd had nothing to do with it since entering parliament and received no benefit from the sale.

Mr Joyce said the federal government had acted on a recommendation from the Queensland government, which confirmed it had supported the buyback.