Labor joined calls for an explanation after it was revealed in Parliament that the department's chosen independent valuer said the official, who negotiated to pay a 20 per cent premium above the upper range of his valuation of water from two Queensland properties, was not acting on his advice and the inflated price was "not reasonable".

Independent senator Rex Patrick used parliamentary privilege on Tuesday to name the official who he says negotiated the higher purchase price - Mary Colreavy, an assistant secretary in the department now responsible for governance in environmental approvals.

Senator Patrick said in his speech that he was told that after Colliers International had not advised the inflated price, the Auditor-General Grant Hehir asked the department to review what it knew at the time of the negotiations.

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Mr Hehir wrote to Senator Patrick this month saying the department may not have made the decision to do so if it had known that view at the time.

But the department disagrees, telling The Canberra Times it has considered all material and found nothing that would alter its approach or decision.

"The department has confidence in the conduct of all staff with regard to this matter and will not be responding to calls by Senator Patrick to take any action against individual staff members," a spokesperson said.

In a speech to the Senate on Tuesday night, Senator Patrick called for Ms Colreavy to "resign or be fired", saying the error was incompetence and she had carriage of the sale from start to finish.

"We can't have these sorts of mistakes just being brushed over," Senator Patrick said.

"Ms Colreavy must resign. If she does not, she must be fired."

He said Ms Colreavy had demonstrated incompetence to the tune of $13 million, and her departmental secretary Andrew Metcalfe should see her removed.

"If her departmental secretary, Mr Andrew Metcalfe, does not see that she is removed then he should go as well because the standard you walk past is the standard you accept, and this sort of incompetence is quite unacceptable," he said.

The government purchased the water from the two Queensland farms in 2017 in a deal with Eastern Australia Agriculture worth $80 million as part of a program to support targets in the Murray Darling Basin Plan.

Last year an audit of the water buyback scheme was scathing of the application of policies to secure taxpayers value for money. The program was scrapped by the government this month after it failed to deliver on expectations.

Shadow minister for the environment and water Terri Butler said Prime Minister Scott Morrison must explain the series of scandals that included sports rorts, Leppington Triangle airport land rorts and payments to multiple companies linked to government minister Angus Taylor that have previously been raised in Parliament.

"How can Australians trust this government to get things right when they're learning that the department has managed to pay so much money to this company for these water entitlements?" Ms Butler asked.

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