Mayor Brandon Johnson’s administration said Friday he will move forward with evicting migrants out of city shelters after they’ve stayed 60 days — but will be granting a reprieve for residents affected by a measles outbreak in a Pilsen migrant shelter and families with children.

Going forward, migrants will also now be required to be vaccinated for measles, mumps, rubella and chickenpox — and will not be allowed into shelters if they refuse vaccination or cannot provide prior proof of vaccination.

More shelter sites will also be exempt from the deadlines if confirmed cases are found, and for those having to quarantine.

Systemwide, families with children will receive a 30-day extension, which can be extended three times through June 10 — shortly after the Chicago Public Schools year ends, city officials announced.

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Despite the new exceptions that will be allowing thousands to extend their stays, city officials said 35 people will still have to leave three shelters on Sunday and find their way to the city’s landing zone and request another spot for shelter. Altogether, 2,026 will be required to leave by the end of April.

The looming deadlines have led to a scramble for migrants to find housing — with thousands no longer receiving the help of a state rental assistance program.

“We want to try to minimize those disruptions as much as possible while we do have this space in this moment. So there may be more,” Johnson’s First Deputy Chief of Staff Cristina Pacione-Zayas said of additional extensions. “I think you can go ahead and talk to [Republican Texas] Governor [Greg] Abbott to see what his plan is, because it’s unknown from us, from our perspective.”

Since the 60-day shelter stay limits were announced last year, Pacione-Zayas said 6,700 people have been resettled with the help of Catholic Charities and New Life Centers, while 2,365 have left Chicago or Illinois altogether. Another 4,155 people currently in shelter are still eligible for a state rental assistance program.

The start of evictions comes as more than a third of the City Council asked the mayor to scrap the policy altogether. But Johnson reiterated at an unrelated press conference earlier this week that the city’s shelters are intended to be temporary and that there are already exceptions to the policy, such as those who have a pending lease or have health issues.

“We’re providing temporary emergency shelter with the goal and the expectation that people can move on,” Johnson told reporters Wednesday. “So there are a number of people who won’t be subject, because they fall under that particular dimension of the policy.”

The hard-line policy was first announced in November as the city attempted to more quickly move people through an overwhelmed shelter system. But as winter moved in, the mayor kept delaying the deadline due to freezing temperatures.

A WBEZ analysis previously found the majority of migrant shelter stays are longer than 60 days, with the longest stays lasting more than a year. Pacione-Zayas said Friday, the average length of shelter stay is now roughly 94 days.

The city has experienced a downturn in people arriving in recent weeks, with a little over 11,200 migrants staying in 23 shelters. Another 43 are currently waiting for a spot at police station lobbies and the city’s designated landing area, a Near West Side site where buses are directed to drop people off.

But crowded conditions at shelters have persisted, and city officials have repeatedly warned of an expected influx of migrants ahead of the Democratic National Convention in August.

Twenty-two alderpersons, City Clerk Anna Valencia and dozens of community organizations sent a letter earlier this week urging Johnson to abandon the eviction policy. Instead, they asked for shelter stays to be determined on a case-by-case basis along with calling for more funding for a state-administered rental assistance program and a federal expansion of work permits for asylum seekers — and longtime undocumented immigrants.

They warned migrants forced to leave would be at risk of homelessness and that public health concerns from the recent measles outbreak will be amplified if the evictions are carried out.

“We need an end to this policy, as it doesn’t solve our challenges, it merely exacerbates and displaces them,” read the letter, led by Ald. Andre Vasquez, 40th Ward and chair of the Committee on Immigrant and Refugee Rights.

The city’s largest shelter, a former warehouse in Pilsen where a 5-year-old boy died from sepsis last year, has now been the site of a measles outbreak. It’s the first time a case of measles has been reported in the city in five years. A team from the Centers for Disease Control and Prevention has been in Chicago as the city works to vaccinate residents at additional shelters and those just arriving to the city.

Vulnerable shelter residents, like those who are pregnant or infants under 1-year-old, have been being moved to other spaces, like hotels. As of Thursday afternoon, 98 people, including 48 children, were being housed in a Chicago-area hotel to quarantine, according to a news release from the Illinois Department of Public Health. Newly vaccinated shelter residents have been asked to quarantine for three weeks until they are fully immunized.

“It’s just a perfect storm. People are sleeping very close to each other. There’s a little bit of space, but it’s not very much space. It’s like a giant slumber party,” said Evelyn Figueroa, a professor of family and community medicine at University of Illinois Chicago, who was in the shelter Sunday night. “That means that the people that are in that perimeter are very at risk unless they are vaccinated.”

For the first time Sunday, volunteers with the Mobile Migrant Health Team were permitted into the Pilsen migrant shelter to help administer measles vaccines. Volunteers were on site from 4 p.m. to past midnight, and Figueroa, who serves as the volunteer group’s medical advisor, said the desperation is palpable.

“I had a man yesterday night, who just said, ‘If I can’t work, I’ll live outside then on a piece of cardboard. I have to. I’ve finally gotten a job. I’m not losing my job,’” Figueroa said. “He’s like, ‘We can’t stay here anymore. We can’t live this way anymore.’ And he goes, ‘You understand, we almost killed ourselves to come here. It’s going to have to get better than this.’ And I could completely hear him.”

Jenn Torres, a mutual aid volunteer, said some migrants eligible for housing assistance are leaving before they can get the help out of fear of getting evicted and worries there won’t be enough information for them once they are evicted.

“Are they giving transportation through OEMC? Are they giving Ventra passes? Like, I am pretty unclear at what information residents are getting,” Torres said.

WBEZ’s Adriana Cardona-Maguidad contributed to this report. Mariah Woelfel and Tessa Weinberg cover Chicago politics.