A federal appeals court sided with the city Monday night, saying it can force employees to get the vaccine or take an unpaid leave.
The deadline is Friday.
As CBS2's Lisa Rozner reports, without the first shot by 5 p.m. Friday, employees will not be allowed at school.
Right now, 13% are not vaccinated, and Rozner spoke with one of the employees who will not cave.
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"This is the hardest decision I've ever made in my life, but I feel like it's an important one," said Bronx history teacher Stephanie Edmonds.
Edmonds says she fought hard for schools to reopen last year, so students could get a better education. But now, she'll have to say goodbye to those she's mentored the past six years.
"I will not be coerced into inserting something into my body that does not fall in line with my religious faith," Edmonds said.
Edmonds is one of around 3% of teachers the union are not vaccinated.
Come Monday, the mayor says thousands of substitutes are ready to fill jobs like hers. But the third of school safety agents who are not vaccinated cannot be replaced.
"There is overtime which will help us to fill some of those shifts. There's places where if you had a number of school safety agents and have one less, it doesn't stop you from getting the work done," said Mayor Bill de Blasio.
Staten Island Councilman Joe Borelli says Tottenville High School, with almost 4,000 students, is already seeing unvaccinated staffers reassigned.
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"I'm trying to get an answer out of the DOE how losing three security agents at Tottenville High School is making Tottenville High School safer when the security agents were already tested and screened for COVID this week. We know they don't have it," Borelli said.
Greg Floyd leads Local 237 Teamsters, the union for school safety agents, and is encouraging members to get vaccinated, but doesn't want them to lose work if they don't.
"I also saw the police department, and I've never seen this before, send out text messages to our members, notifying them of a 6:00 a.m. schedule to 6:00 p.m.," Floyd said. "The members who got vaccinated and did the right thing in this situation are being punished by having a 12-hour tour."
The union for school school supervisors and administrators says if the mandate went into effect Tuesday, "there would have been too many schools and early childhood centers unable to operate safely."
It's urging the DOE to quickly address staffing concerns this week.
Meantime, the union representing cafeteria workers and custodians is echoing Borelli's request, which is to continue to implement weekly testing instead for the unvaccinated.
"They left these administrators with no plan of attack with how to make up services. This was poorly thought out, poorly executed," Borelli said.
"On a normal day, we serve 900,000 meals, and without staff to do that, it is nearly impossible to do," Donald Nesbit, vice president of the cafeteria workers' union, told CBS2's Ali Bauman.
Watch Lisa Rozner's report --
Frozen pineapples and cold chickpeas are some of the pre-packaged grab-and-go meals parents say schools have been serving for lunch this month.
Some schools temporarily switched to a cold menu during the pandemic, and Nesbit says students should get used to it because the city could lose up to 30% of its cafeteria workers next week when the vaccine mandate takes effect.
"That is the plan, that everything goes to being cold and pre-packaged. We have never saw anything like this, so I question the quality of lunch that is actually going to be there for our students," Nesbit said.
For those positions like cafeteria cooks and safety agents that are harder to replace, the mayor believes the vaccine holdouts may eventually change their minds.
"I think you're going to see people start to come back when they actually experience not having a paycheck," he said.
In the meantime, the DOE insists cold meals have the same nutritional value as hot meals.
Attorneys for unvaccinated employees are planning to ask the Supreme Court to hear their case by Friday.
De Blasio says in the last 24 hours, 1,000 more people got the vaccine.
CBS2's Lisa Rozner contributed to this report. Editor's note: This story first appeared on September 28, 2021.
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