The movie star was snapped earlier yesterday when the helicopter he was travelling in landed at the airport to refuel, said the photographer, who didn't want to be named.
"He's been in a helicopter since 9 o'clock this morning (Monday), just flying around the whole of the Wakatipu. He's back out there now," he said.
While the chopper was refuelling, Cruise could be seen inspecting the aircraft.
"He looked happy, definitely curious about the helicopter . . . he's curious about checking out the parts on it, you could see him checking out the rotor blades and the detail of it. Beautiful-looking helicopter."
The photographer said Cruise was happy, smiling, and giving the thumbs up to staff.
He was wearing a black New York Yankees hat.
Co-stars Henry Cavill and Simon Pegg are also in New Zealand. Excited fans have been taking to social media to share photos of themselves meeting the stars.
"Soooooo just met superman," Instagram user Sammii Whittles said, posting a photo of Cavill with a group of young women.
Scientology New Zealand secretary Mike Ferriss said the church had no information about Cruise visiting New Zealand.
"On several occasions celebrity members of our church have travelled to NZ, but we make no special arrangements for them as we do not involve ourselves in the private lives of our members," Ferriss said.