The airline said it had agreed to remove a scene from the video featuring All Black centre Richard Kahui politely turning down a request to give gay flight attendant Will Coxhead a peck on the cheek.
"The move comes after complaints from members of the gay and lesbian community in the past week," Air New Zealand said in a statement.
The flag carrier said a university professor, whom it did not name, had raised concerns the homosexual rejection could lead to gay male suicides.
The light-hearted video called "Crazy About Rugby" shows All Blacks running through safety procedures for passengers boarding Air New Zealand flights.
The offending scene had All Black pin-up Kahui posing for photographs with female flight attendants then shaking his head, holding up his hands and refusing to pucker up when Coxhead points to his cheek hoping for a kiss.
The airline's operations and safety manager David Morgan said it had not anticipated the scene being viewed as distasteful or causing concern.
"We have opted on the side of caution and are changing out the scene," he said.
Coxhead, a real-life flight attendant with the airline, said he was "absolutely gutted" at the complaints over a scene he described as a bit of fun.
"I’m proud to be gay, proud to be an Air New Zealander and extremely proud of my role in the safety video," he said.
"Obviously there are some people in the gay community that can be a little precious and need to lighten up."
What the stars mean:
★ Poor ★ ★ Promising ★★★ Good ★★★★ Very good ★★★★★ Exceptional