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Looming deadlines and threats of termination have convinced hundreds of hesitant health care workers to get their COVID-19 shots in recent days, but thousands of holdouts remain, Massachusetts hospital leaders reported Friday.

Already, one major hospital system, Springfield-based Baystate Health, said it terminated 90 workers who remained unvaccinated on Friday after an extensive effort to change their minds.

A pressing deadline also looms at Mass General Brigham, the state’s largest hospital system, where still-unvaccinated employees will be placed on unpaid leave at the end of their shift on Wednesday, the company said. Roughly 1,900 employees — about 3 percent of the 80,000-person workforce — remained unvaccinated Friday, or had failed to submit documentation showing they had received at least one shot, according to the company.

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“We are mandating the vaccine because we want to do everything possible to protect you, your families, and our patients,” the company said in a memo Thursday to employees. “You make our system great, and we do not want to lose you as a result of this condition of employment.”

It will take several days to sort through all the workers’ documentation, so officials won’t have a solid number of who has not complied until at least Monday, according to Rosemary Sheehan, chief human resources officer at Mass General Brigham. Then, she said, hospital officials will call each employee shown not to be vaccinated, before placing anyone on unpaid leave.

About 800 of the 1,900 still unvaccinated are per-diem workers who don’t have regular hours, so Sheehan said the hospital is focusing on the remaining 1,100.

Hospitals in Massachusetts and many parts of the country are requiring employees to get their shots to protect patients and co-workers from the spread of the virus, and to help bring an end to the pandemic.

The vast majority of health care workers rolled up their sleeves when vaccines became available, but a small fraction are so opposed that they’re willing to lose their jobs.

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The high stakes standoff comes amid an already-acute worker shortage that has made hospitals fearful of losing more staff. Several Massachusetts hospitals have delayed vaccination deadlines through October and in some cases to Dec. 1, allowing more time in hopes reluctant workers will change their minds. But they say that ultimately holdouts will be let go because safety will be the bottom line.

It’s not just hospital workers who face looming vaccination deadlines. Thousands of state employees are required to have their shots by Sunday or risk being suspended or fired.

The state vaccine mandate, announced by Governor Charlie Baker on Aug. 19, applies to about 42,000 executive department employees and 2,000 contractors, whether they are working in person or remotely. So far, state officials say, more than 40,000 employees have either provided evidence of vaccination or applied for an exemption.

Officials at some major hospitals made it clear they are reluctant to fire people.

Beth Israel Lahey Health leaders on Friday eased their deadline to give the vaccine refusers more time. The company had set an Oct. 31 limit for workers to complete their shots or be terminated, but now tells workers they only need to get their first shot by that date.

The company said that 93 percent of the system’s 36,000 employees are vaccinated. That still leaves about 2,500 unvaccinated employees.

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In the Wellforce hospital system, which includes Tufts Medical Center, 98 percent of workers are vaccinated, including 50 who got their shots in the last week. But 275 still remain unvaccinated, said spokeswoman Brooke Hynes.

Unvaccinated Wellforce employees have been placed on leave until Nov. 1, and if they aren’t vaccinated by then, they will be terminated, Hynes said.

At UMass Memorial Health Care, about 88 percent of workers have been vaccinated, a company spokesman said. About 1,900 UMass workers remain unvaccinated or have an accepted religious or medical exemption.

After Nov. 1, unvaccinated workers who do not have an approved exemption will have two weeks — until Nov. 15 — to get at least a first dose. If they do not hit that deadline, they will be put on a two-week leave without pay.

On Dec. 1, any UMass Memorial employee still without at least a first dose, or who does not have an exemption, will be terminated.

“We’ve struggled with [this decision] for weeks, UMass Memorial Health Care said in a memo to employees Thursday. “We want to give all our unvaccinated caregivers every opportunity to get vaccinated and do so with compassion and respect and not have anyone lose their jobs, while also weighing the responsibility of providing a safe environment for our patients.”

At Boston Medical Center, 97 percent of the hospital’s 9,500 employees and faculty on Friday were in compliance with the company’s vaccine mandate. Hospital spokesman Dave Kibbe said workers had until the end of Friday to submit documentation of compliance, and the hospital expected the percentage of those vaccinated would rise.

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Those not vaccinated will be terminated, he said.

Baystate Health officials said more than 99 percent of the workforce received their shots by the company’s Oct. 1 deadline. The company had placed 145 unvaccinated workers on unpaid leave pending the Oct. 15 final deadline to get their shots or be terminated.

By Friday, 90 workers remained unvaccinated, including 52 per diem employees, and they were let go, Baystate said.

At the Dana-Farber Cancer Institute, 99.6 percent of the workforce is vaccinated, the company said Friday. Just 34 people have not started vaccination and remain suspended without pay.

Meanwhile, at Mass General Brigham, one thing is clear: Employees who have not received at least their first shot by Nov. 5 will be terminated.

“We walk a fine line between educating and making people feel like they have been pressured,” said Sheehan, the human resources chief. “It’s been very challenging.”


Kay Lazar can be reached at kay.lazar@globe.com Follow her on Twitter @GlobeKayLazar.