A hateful vandal carrying a rainbow flag defaced at least three New York City churches with “anti-Christian” graffiti, according to cops still hunting the suspect.

The Pride flag-carrying suspect was also wearing a rainbow face covering when cameras caught them vandalizing the churches in Far Rockaway, Queens, in the early hours of Oct. 5, the NYPD said of the hate crime.

The suspect — who was seen pushing a bicycle — first targeted the Refuge Church of Christ at 18-37 Mott Avenue, scrawling the words “anti-gay cult” in black spraypaint on the facade around 1:40 a.m., police and sources said.

Four minutes later, the same perp wrote the same message on the City of Oasis Church of Deliverance, which is about 100 feet away at 18-74 Mott Avenue.

Then, around 2 a.m., the vandal struck St. Mary’s Star of the Sea Church at 19-20 New Haven Avenue. 

This time, “Welcome Cult Members” and “cult” were crawled on the church walls and sidewalks and additionally painted over the faces of two religious statues there, cops and sources said.

Father Francis Shannon, who has been a priest at St. Mary’s Star of the Sea Church for over eight years, said he woke up Tuesday morning to pictures of the graffiti. 

“It was really heartbreaking learning about the vandalism. I was at my mother’s house, and as soon as it happened, I got sent pictures. So when I woke up, I saw them, and it was just really sad,” Shannon, 67, told The Post.

“I think this is more of a statement than a hate crime, so just an anti-institution kind of stuff,” he said.

Shannon maintained that he doesn’t believe the hateful scrawlings represent the actions of the entire LGBTQ community, and encouraged the vandal to engage in dialogue instead. 

“I don’t think this is a big part of the LGBTQ movement since he had the flag. I think he’s just the exception,” Shannon said.

“I just think he needs to talk it out and to not act on it with violence.” 

The NYPD Hate Crime Task Force is investigating it as “multiple acts of criminal mischief as a hate crime.”