Australia’s top infrastructure bureaucrat has vowed to get to the bottom of why the federal government paid more than $30 million for land worth $3 million.

The Western Sydney Airport deal is being scrutinised at Senate estimates after the Australian National Audit Office excoriated the purchase in a scathing report.

Infrastructure Department boss Simon Atkinson agreed it appeared officials had tried to cover up the issue when auditors started hunting for answers.

“I want to get to the bottom of what happened, which is why I’ve pulled in an independent auditor of my own so that I can get to the bottom of the facts,” he told a hearing in Canberra on Monday.

“I’m trying to clean it up.”

Former intelligence chief Vivienne Thom is investigating one public servant over the Leppington Triangle land deal.

Another officer is facing a separate investigation over allegations conflicts of interest were not declared on other matters.

Mr Atkinson moved to refer it to the Australian Federal Police on October 8 but found the ANAO had already sparked an investigation.

He said the auditor-general’s report contained very concerning allegations which he took extremely seriously.

Labor’s chief questioner Penny Wong described the auditor-general’s report as a damning indictment of the department.

“I actually find it gobsmacking,” she said.

Senator Wong said the report uncovered extraordinary conduct that was outside what any reasonable person would think was appropriate.

“But worse, what it looks like is people tried to cover it up when the audit office came asking questions,” she said.

The report found the department did not show appropriate due diligence in paying $30 million in 2018 for the 12-hectare plot, which was worth only $3 million.

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

The audit found property owner Leppington Pastoral Company had suggested to the government the name of a valuer, which was agreed to by the department.

Mr Atkinson has also flagged a review of the department’s culture and processes.

Deputy Prime Minister Michael McCormack, who is also infrastructure minister, insists the purchase was a bargain for taxpayers.

But the department secretary wouldn’t be drawn on that assessment, saying it was hard to know if compulsorily acquiring the land would have cost more.