New York City Transit President Andy Byford unveiled a crackdown on subway vagrants Monday — directing station managers to remove homeless people who take up multiple seats and make a mess.

“There is a fundamental difference between someone coming in to keep warm and sitting on a seat and dozing off, I don’t really have a problem with that,” Byford said at an MTA board meeting the board. “But laying across a seat or behaving in an antisocial manner or making a mess is not acceptable.”

Byford told staffers to leave people alone on a train or in a station if they are in a single seat, but to call the cops if the vagrants are engaging in “antisocial” behavior.

Byford, who installed dozens of new station managers across the system last month, has ordered them to crack down on several elements that make the subways unpleasant — from graffiti to pigeon poop to dirty benches.

After being told about the tough new policy, board member Charles Moerdler cautioned Byford to be aware of the precarious position that homeless people are in.

“They are human beings,” Moerd­ler said. “They are individuals with individual problems. To deal with them all as one is just wrong, and to deal with them uncaringly and recklessly, in my view, is a disaster.”

Byford replied that he will tell station managers to exercise care, but that he isn’t going to let the homeless affect the comfort of other riders.

“We have a responsibility to provide our customers with a safe, pleasant, ambient surroundings,” Byford said.

“We equally have to make sure that people are not causing offense to other customers or making a mess,” he added.

The NYC Transit chief later put out a statement tempering his tough talk, insisting, “We firmly believe that New Yorkers who are homeless are human beings with individual problems who must be treated compassionately.”

But, he added, “We also must ensure clean and safe conditions . . . for all of our customers.”

Advocates for the homeless panned Byford’s approach.

“What he’s saying is unhelpful overall,” said Giselle Routhier, policy director at Coalition for the Homeless. “The approach should be relationship-building and offering people services.”

Riders said they don’t think the MTA should call the cops on homeless people for lying down in stations and on trains or carrying all their possessions around.

“You just can’t clear them away and send them nowhere,” said rider Shelly Reynolds.

“They are homeless, without resources,” she added. “I think that you have to have an alternative plan for homeless people.”

New York City currently has a record number of homeless, with at least 62,166 people currently out on the streets, according to statistics from the summer.

Additional reporting by Shari Logan