A plan to clear homeless people from New York City subway trains in a pre-dawn Monday operation by police and transportation officials was abandoned amid pressure from campaigners.

Dozens of homeless men and women sleeping on the seats of E line trains as they rolled into the World Trade Center terminal in the early hours were left alone, despite warnings that they would be asked to leave so cars could be cleaned.

“It was postponed,” Kevin Ortiz, a spokesman for the Metropolitan Transportation Authority, told the Guardian. “We decided not to go ahead. I can’t give you a specific reason why it was postponed. But it may well take place in the future”.

Detective James Duffy, a spokesman for the New York police department, said in an email: “I’ve learned that the MTA operation for this morning was cancelled”.

City officials told DNAInfo last week that from 3am on Monday, each E train pulling into World Trade Center and the Jamaica terminal at the other end of the line in Queens would be entered by teams of medical staff, police officers and MTA officials.

Other lines were due to be dealt with similarly after the E, which has been the subject of numerous complaints from commuters. The line is particularly popular among sleepers in winter, because it runs 24 hours a day and is completely underground.

Amid sharp criticism, officials clarified that the plan was for an “outreach program” to help homeless people during cold weather. They stressed that no one could be forced to leave the subway system unless they were hurting someone or committing a crime.

“We offer extensive services, ranging from providing them with shelter to helping them if they are sick,” Ortiz said later on Monday.

However, no police or any other officials were at the World Trade Center stop at 3am. Trains carrying a number of sleeping people arrived, idled for about 15 minutes, then set off in the opposite direction.

Volunteers from Picture the Homeless, a group that campaigns for the rights of homeless people, had gathered on the platforms of both stations and were travelling the line to ensure that sleeping people were not mistreated.

“The media attention and all the hubbub probably made them [the MTA and NYPD] stay away,” said Sam Miller, an activist with the group. “But [NYPD commissioner Bill] Bratton has a record of things like this. We expect them to try again another day when we’re not expecting it.”

Picture the Homeless held a rally outside NYPD headquarters on Sunday, along with the New York Civil Liberties Union, other advocacy groups and members of the city council. They demanded that the constitutional rights of homeless people be respected.

Some 52,000 homeless people were living in New York City shelters by the end of 2013, according to Coalition for the Homeless, with thousands more living on streets. The number of homeless people living on the subway system has risen from 1,000 in 2009 to more than 1,800 last year, according to a survey by the city’s department of homeless services.

The number of homeless people sleeping on the New York subway system is increasing, according to a city study. Photograph: Jon Swaine/The Guardian Photograph: Jon Swaine/The Guardian

One passenger, John Theo, said early on Monday he had been sleeping on the E train for the past five months and had been homeless for five years. He said he was aware of the plans to clear the trains and had been worrying on Sunday night.

“I would have tried not to go, because I think they would have locked me up,” Theo, 60, told the Guardian. “They won’t help me with housing, so what can I do? They tell me go back to the shelter but it’s dangerous there. Kids want my belongings.”

Theo, who wore a black beanie hat bearing a “New York” logo, said he became homeless after he lost his job as a factory worker and could not find another. His elderly mother is seriously ill in hospital in Stamford, Connecticut, he said.

At 3.28am, as he shut his eyes and tried to steal a couple more hours of sleep before the morning rush, the doors of his car closed and his train headed back towards Queens.