A fox that is thought to have mauled nearly 30 little penguins at Manly's North Head has been shot overnight.

An autopsy on the fox will be undertaken at Taronga Zoo to confirm it was the animal that killed 26 birds over the past 11 days, evading baits, traps and snipers.

NSW National Parks said the North Head little penguin colony is the last remaining on the New South Wales mainland.

NSW National Parks regional Manager Peter Hay said staff and volunteers first discovered the penguin deaths near nesting areas more than a week ago.

"It was devastating for parks' staff and community volunteers who spend so many hours looking after the little penguins," he said.

"This population has proven over time that it can withstand attacks of this nature and recover, and we believe it will fully recover."

Mr Hay said that while the latest development was a good outcome, the operation would continue until there was no further evidence that a threat remained to the colony.

"While this is a positive result we will continue the operation, and monitor the little penguin colony closely, until there is no further evidence that another fox is hunting in the area," he said.

"The network of staff, fox and seabird experts, and community volunteers will continue to work around the clock to protect the endangered colony with the breeding season now underway, and a number of penguins already sitting on eggs."