Mr Dutton also signed off on the internal budget measures, including sacking contractors and casual staff, after being warned the changes would affect the performance of the department and the Australian Border Force, documents obtained under freedom of information laws show.

Late on December 11 last year, The Sydney Morning Herald and The Age revealed that the Border Force planned to save money on fuel by pulling ships from ocean patrols.

The report was prompted by a leaked Border Force email informing staff that "operational limitations" would be imposed to achieve a saving in the annual fuel budget and "ships will cease active patrolling to achieve this fuel saving".

The directive was part of a suite of measures to correct huge overspending by the department last year believed to total hundreds of millions of dollars.

On December 12, Mr Dutton said the fuel savings had not been sanctioned by his government and "I've given very specific direction to the Australian Border Force commissioner that we won't be reducing those patrols at all".

"There will be no reduced presence on the water, we have been very clear about that," he said.

But internal Home Affairs documents marked "Protected: Sensitive" show that on December 11, Mr Dutton signed off sweeping internal budget savings measures across the department, including Border Force.

The document, titled 2018-19 Departmental Budget Update, outlined Home Affairs' budget position and the steps needed to ensure "the alignment of planned activity ... with current funding levels".

It included changes to Border Force operations to meet budget restraints while "minimising the impact on front-line operations".

Large parts of the document have been redacted and it is not clear if it specifically outlined cuts to ocean patrols.

However the document shows Mr Dutton noted the broad spending changes and did not seek to discuss them further with officials.

This is despite the document warning that "the implementation of these measures will impact the department and ABF's planned performance levels".

The document also outlined plans for an "immediate freeze" in engaging new contractors and consultants including spending on "major corporate contracts that underpin core functions".

Money would also be saved by "stopping and slowing" planned project spending and limiting staff travel.

Grilled about the cuts to ocean patrols at a Senate estimates hearing in February, Border Force Commissioner Michael Outram said the measures described in the staff email were a proposal only and "nothing happened".

He was later forced to correct the record, conceding that between December 3 and 11 last year the agency's vessels adopted "a more risk-based approach" where their activities were "cued through intelligence, radar sighting or visual sighting". Border Force insiders say this means boats were not actively patrolling, but waiting to be deployed if suspicious activity was otherwise detected.

The correction contradicted Mr Dutton's claims that the agency did not reduce its marine presence.

News of the cuts to patrols undermined a Morrison government attack on Labor late last year over its support for proposed changes to medical evacuations from Nauru and Manus Island, which the government said threatened national security.

Mr Dutton's office did not respond to repeated requests for comment.

In December, Mr Dutton said the department must operate within its funding and denied the government had cut the department's budget.

Labor's Home Affairs spokeswoman Kristina Keneally said the revelations "go to the heart of [Mr] Dutton's mismanagement of his department and his neglect of his ministerial responsibilities".

"Mr Dutton stood before the media and declared there were no budget cuts to his department the day after he had signed off on measures to recoup a $300 million budget black hole that had happened on his watch," Senator Keneally said.

"How wide and deep would have Mr Dutton been willing to slash his department's budget if these measures ... had not been exposed in the media?"

Senator Keneally said the measures would have weakened Australia's border protection.