Detective Warwick Webber of Rotorua police said a 25-year-old Rotorua man had been arrested on Friday. He was facing five charges of making inappropriate visual recordings.
Police also seized the man's computer and storage devices during a search of his home on Friday. They did not believe any other toilets were involved.
Webber emphasised Starbucks was the victim and hoped people would not boycott the cafe franchise giant.
A staff member, who did not want to be named, said about three customers had been recorded.
Regular customers had recalled seeing a man in the toilet queue letting people go before him.
They told staff he had taken a long time in the toilet then "hurriedly" walked out.
"It's pretty disgusting," the staff member said.