City officials said that starting Monday, they will begin removing homeless people from the E train. View Full Caption DNA/Stephanie Keith

QUEENS — The NYPD and the MTA plan to clear homeless men and women out of the subway system after a skyrocketing number of people have sought shelter there from the brutally cold winter, police officials said.

The plan, which is set to begin before dawn on Monday, comes amid an upswing in homeless people in the subway system during the exceptionally cold winter. There were more than 1,800 people living on the subways in 2013, up from 1,000 in 2009, according to the city's annual HopeNYC street survey.

Starting Monday at 3 a.m., teams of transit workers, NYPD officers and emergency medical technicians will go to the E train stations at Jamaica Center and at the World Trade Center, officials said.

Each time a train pulls into one of the two stations, teams will check each car, and take all the homeless people inside to either a shelter or hospitals, officials said.

The trains will then be cleaned for the morning rush hour.

"We are not doing this to be cruel to them," Christie Hofmann, a New York City Transit official, said at a Wednesday night meeting. "[Homelessness] is not going to get solved overnight, but we are working on it together with police officers."

The initiative was partly launched to help improve conditions for other riders, officials said. The operation will begin on the E line, where the problem is most visible, and will later move to other subway lines throughout the city, officials said.

“It’s going to be a really comprehensive effort to alleviate the homeless condition that we have,” said Deputy Inspector Michael Telfer, who oversees Transit District 20, which covers part of Queens.

Gene Russianoff of the Straphangers Campaign said he had a number of concerns about homeless people in the subway system which, he noted, "is not a place for people to live.”

He said homeless people riding the trains are often victims of crime and are exposed to numeorus dangers when they move from one car to another while trains are in motion.

He also said that there are a lot of hygiene-related issues that are problematic for other passengers.

The initiative comes on the heels of a $6 million MTA outreach program and a 90 percent increase in the homeless population in the subway, according to the Daily News.

The MTA referred questions to the city's Department for Homeless Services, which did not immediately comment. The NYPD did not immediately respond to a request for comment.

The mayor was not involved in the decision and does not have details about the plan, according to City Hall sources.