The Mail on Sunday said the 2.99 pound ($4.65) app allowed it to keep close track of William as he flew in his capacity as a private pilot with East Anglian Air Ambulance in eastern England.
It said the app allowed its journalists to pinpoint where the country's future king was planning to land the air ambulance helicopter.
It published photos appearing to show William's helicopter landing and of the prince himself talking to colleagues on the ground.
For a small extra fee, the newspaper said, users could receive a text alert every time the helicopter William uses takes off on a mission.
"Most of the time when an air ambulance is called it appears on the scene, scoops someone up and disappears," he said. "If there were someone monitoring, the chance of them being there at the scene when he arrives is quite remote. And we don't know from one day to the next if he's going to be on board. So I don't see a problem."
William's press office refused to comment, calling it a security matter. The Metropolitan Police also refused to comment.