The federal government paid $30 million for a 12-hectare plot of land worth $3 million under a deal uncovered through a scathing auditor-general's report.

Deputy Prime Minister Michael McCormack raised eyebrows on Monday when he predicted it would be seen as a bargain in the future.

But Mr Morrison is taking the side of the National Audit Office.

"I understand why Australians would feel very disappointed in that. I'm also disappointed in it," he told reporters in Canberra on Tuesday.

"I don't think it's something that I would ever like to see repeated."

While he split with his deputy over the land purchase, he insisted there was agreement on the merits of Sydney's second airport.

"This is a megalithic project for western Sydney, and for Sydney more broadly and the country," Mr Morrison said.

"The deputy prime minister and I are on the same page when it comes to that, but when it comes to the processes that led to that decision, I'm not happy about it."

The department has since appointed an independent investigator to examine the land deal and staff conduct throughout the purchase.

The auditor-general found the department did not show appropriate due diligence and fell short of ethical standards.

It paid 22 times more per hectare than the NSW government spent on its portion of the land.

The department has agreed to improve the way it gets valuations, prepare more detailed cost-benefit analyses and run proper meetings with landholders.

Mr Morrison said officials were aware of his disappointment.

"Now that it's come to light and has been brought to our attention, we'll be ensuring it won't happen again," the prime minister said.

Australian Associated Press