A Brooklyn teaching assistant is suing the city Department of Education claiming he was wrongfully fired following a botched investigation into claims he kissed three young girls.

Former paraprofessional Grigoriy Zagerson was canned from PS 195 on Sept. 17 “based on a faulty investigation and motivated by discriminatory animus” of the school principal and investigators looking into claims that he kissed two 6-year-old girls and an 8-year-old girl on the cheek, according to his Manhattan Supreme Court lawsuit.

The 55-year-old Brooklyn man — who started at the Manhattan Beach school in 2010 — said he was suspended without pay in March 2018 over the allegations.

One girl, who was 6 at the time, told investigators that Zagerson “commented on her smile and then kissed her on the cheek,” court papers said.

A second girl — who had witnessed the first incident — told investigators that she was upset after he corrected her on an assignment and “Zagerson then pulled her toward him by the arm and kissed her on the cheek” too, the documents said.

A third girl, then 8 years old, said Zagerson also kissed her on the cheek on several occasions, according to documents that accompanied the lawsuit. The educator was helping the girl — a native Russian speaker like him — learn English.

Zagerson admitted to investigators that the Russian-speaking girl had once hugged him and told him she missed him “and added he may have ‘pecked’ her cheek.”

He also insisted he didn’t remember kissing the other two girls but said he “may have ‘pecked'” one of them on the cheek when she arrived at school upset, the court filings said.

“If a student chooses to approach me and hug me, I cannot physically block them or pull them away in a manner that would constitute corporal punishment,” Zagerson said in response to the investigators’ findings. “What I can do, and have done countless times, is remove myself from the situation, as quickly and gently as possible, without causing additional emotional harm to the student in question.

“This is the worst of my transgressions — which I do not truly believe were transgressions,” he added in his response.

“I am not a child abuser or a pedophile, and I will take whatever actions are necessary to make sure that my name is not forever associated with these false and defamatory allegations.”

Zagerson is now suing the DOE, Special Commissioner of Investigation for the New York City schools and the DOE chancellor, saying the allegations were mishandled.

He claimed he was never given dates of when the incidents happened, nor provided the girls’ statements, according to court papers.

He also said other adults who were present during the alleged kissing incidents — including two teachers and three other assistants — were never interviewed and neither were any of the other students, the court documents allege.

Zagerson — who claimed he was never alone with any of the three girls — accused school principal Bernadette Toomey of starting her own “flawed investigation” and flouting DOE rules.

Toomey, he alleged, “wrongly construed the allegation as sexual harassment” even though investigators didn’t consider his case sexual harassment.

A union rep told Zagerson that Toomey “was looking to remove him from by the school by any means necessary,” the lawsuit said.

Court filings show that SCI “substantiated” the allegations and recommended firing Zagerson in an August letter to the DOE chancellor.

City Law Department spokeswoman Kimberly Joyce, said, “We will review the complaint and respond accordingly if and when served.”

SCI did not immediately return a request for comment.

“These were troubling allegations that were reported for investigation to SCI, and he was terminated after the Special Commissioner substantiated the claims,” said a DOE spokeswoman. “We will review the suit.”