The family film will not be shown in Kuwait, Oman, Qatar and Saudi Arabia, Hollywood media have reported.
Police officer Specter, voiced by Lena Waithe, has been heralded as Disney-Pixar's first openly gay character.
Her lines include: "It's not easy being a parent... my girlfriend's daughter got me pulling my hair out, OK?"
Other Middle East countries like Bahrain, Lebanon and Egypt are showing the film.
And according to Deadline, Russia censored the scene in question by changing the word "girlfriend" to "partner" and avoiding mentioning the gender of Specter, who is a supporting character.
Speaking to Variety, Waithe explained that the line about "my girlfriend" was her idea.
"I said, 'Can I say the word girlfriend, is that cool?'
"I was just like, 'It sounds weird.' I even have a gay voice, I think. I don't think I sound right saying 'Husband.' They were like, 'Oh yeah, do that.' They were so cool and chilled. And it ended up being something special."
Waithe has also starred in Ready Player One and Westworld, and recently wrote and produced Queen & Slim.
Set in a suburban fantasy world, Onward is about two teenage elf brothers (voiced by Chris Pratt and Tom Holland) who go on an adventure after their mum gives them special gifts from their deceased father, including a letter that can resurrect him for just one day.
Coronavirus: 'Zero impact' on box office
Onward topped the North American box office chart on its opening weekend, with takings of $40m (£30.5m), which was in line with predictions.
Overall box office receipts were significantly down this weekend, but experts don't believe the fear of coronavirus was to blame.
"I think there was zero impact," Paul Dergarabedian, a senior media analyst with Comscore, said.
"With $40m for Onward, a small drop off for The Invisible Man ($15.5m/£11.8m) and The Way Back ($8.5m/£6.5m) getting solid scores from audiences, it looks like people are in the habit of going to the movies."
The virus has forced the release of the next James Bond film to be postponed, with Hollywood waiting to see what impact the outbreak will have on ticket sales for other films.
Meanwhile, more major Hollywood films have encountered problems with censors in conservative countries as more gay characters have been portrayed.
Last year, Russia censored scenes in the Sir Elton John biopic Rocketman and Avengers: Endgame as a result of LGBT references.
In 2017, Disney's Beauty and the Beast was banned in markets including Kuwait and Malaysia over a reference to Josh Gad's character LeFou being gay. Russia gave it an over-16 rating.