He's really down to earth, so it was just nice to have him here and that he would want to come see this."
Cruise was filmed leaving the church building to the sound of cheering and applause, with a security guard blocking a Newshub camera crew.
Cruise was then driven away in a late-model BMW.
The low-key visit came three hours after the Hollywood star has bid farewell to the "amazing people of New Zealand" on Twitter.
The film star arrived in New Zealand last month to shoot the new Mission: Impossible.
Cruise has been a devout supporter of the Church of Scientology for decades, claiming its teachings helped him overcome dyslexia.
The Church of Scientology's $16 million Auckland building was opened by its leader David Miscavige in January.
Earlier, Cruise said goodbye to New Zealand with a single tweet.
Cruise said he'd had "a great time" filming here.
He included a photo of him posing with his co-stars Simon Pegg, Rebecca Ferguson and Ving Rhames.
Cruise has spent a month filming here on a set built to resemble a settlement in Iraq.
His co-stars were more sociable, often posting their off-set activities to social media.
Mission: Impossible 6 is due for release on July 27, 2018.
