The clip shows Milligan leaning in, but cuts abruptly before the kiss is shown, while a shot of two female characters kissing was left unedited.
Levy, who is gay and played pansexual Rose in the series, wrote: "You showed the kiss between two women, you showed the kiss between a woman and a man, then removed the kiss between two men? This is a show about the power of inclusivity,"
"The censorship of gay intimacy is making a harmful statement against that message. #loveislove."
It was a fan who first brought the video to Levy's attention, sharing the clip on Twitter months ago and labelling it "disheartening".
"Thought you should see this. I had no idea they aired Schitt's Creek in India on TV, but I just found out that m/m kisses are censored on Comedy Central, and I know most people there watch it on Netflix, but this is so disheartening," they said, sharing the same promotion tweet, which was posted last year.
"What network TV chooses to show matters."
Throughout its six-season run, the show was praised for the way in which sexuality was represented.
The writing even helped one of its stars come out.
Emily Hampshire, who played Stevie in the show, previously told Gay Times that it taught her about pansexuality — the romantic or emotional attraction towards people regardless of their sex or gender.
"I had to ask Dan what pansexuality was, I didn't know at all. Cut to five years later, definitely pan," she said.
For it's portrayal of the LGBTQI+ community, Schitt's Creek was nominated twice for a GLAAD Media Award for Outstanding Comedy Series, taking home the gong once.
The series also cleaned up at the Emmys in September, winning all major comedy awards and all four major acting categories for its final season.
