The subway conductor charged with slugging a straphanger who put his feet on a seat in the subway on New Year’s Day has been banned from operating trains that carry passengers while the Metropolitan Transportation Authority (MTA) investigates the incident, an agency spokesperson said.

Christopher Thomas, 53, was arrested for hammering an 18-year-old rider, punching the teen in the face and slamming his head on the side of a southbound R train at about 5:50 a.m. on January 1, near the 36th Street station in Long Island City.

A criminal complaint filed by police states that the victim, Zaid Al-Doon, a freshman at SUNY Binghamton, suffered multiple bruises to his head and an abrasion to his face in the beating, but the injuries were not considered serious.

Thomas, who has been on the job since 2007, told police he snapped after arguing with Al-Doon, who was stretching his legs and taking up several seats on a subway car crowded with New Year’s Eve revelers, law enforcement sources said.

Thomas was charged with assault and harassment at his arraignment at Queens Criminal Court, where he was released without bail.

Thomas, wearing his conductor’s uniform under a hooded sweatshirt, told reporters outside the courthouse that he was not at liberty to discuss details of the incident.

“I don’t want to put my job in jeopardy by explaining what happened,” Thomas said. “As per my job, I can’t comment.”

MTA rules prohibit straphangers from putting their feet on seats in the subway – an act that results in a $50 fine.

Straphangers on the R line last week said they were shocked by news of the beating. “It’s crazy,” Jaden Christopher, 38, said. “If this guy didn’t like what the kid was doing, he should have called police and stopped the train. For sure, there were probably police on the train because of the New Year’s Eve celebrations.

“He should have checked to see if there was a cop on board. It wasn’t up to him to hand this guy a beating,” Christopher said.

Thomas has a criminal record that includes a robbery and menacing arrest in 1995 and a 2011 arrest for assault, law enforcement sources said.

An MTA spokesperson said Thomas would not return to his regular assignment until the agency has completed an internal probe into the incident.

“We condemn violence of any kind, whether it is by a customer or an employee,” the MTA spokesperson said.