Home Affairs Minister Peter Dutton has ordered the Australian Border Force to maintain its current level of ocean patrols despite the leak of an internal directive that some ships should stay in port due to a fuel cost-blow out.

On Wednesday, Mr Dutton said Border Force would have to work within its budget, but could rely more heavily on aerial surveillance and Australian Defence Force ships to patrol maritime borders.

His directive follows a statement on Tuesday where he alleged a report by The Sydney Morning Herald and The Age that ABF had ordered a reduction patrols was "inaccurate".

"When you have had a number of surge points throughout the year there is an additional expense and if they are going to have a cost overrun they will look at ways they can manage that," he said on Wednesday.