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Vaccination numbers for city Department of Education staffers continue to rise — but some administrators are still scrambling to fill faculty holes before the Monday morning deadline when the mandate goes into effect.

The DOE said that at least 90 percent of its 148,000 staffers — and roughly 93 percent of 78,000 classroom teachers — have gotten at least one dose of the COVID-19 vaccine as of Friday.

While the city set a deadline for the end of the workday, DOE employees who present a vaccine card Monday morning will be allowed to work inside their schools.

“Vaccination mandates work and ours will help keep our schools safe and healthy,” said DOE spokesperson Katie O’Hanlon.

Only 500 religious or medical exemptions were awarded, O’Hanlon said.

Still, with upwards of 15,000 DOE workers facing removal from payroll, the city principals’ union warned of looming challenges next week.

“Though this additional week has been helpful, we still have concerns about staffing at some schools, particularly regarding safety agents and paraprofessionals,” Council of union chief Mark Cannizzaro said in a statement. “While we’re thankful that the percentage of vaccinated staff has increased systemwide since the deadline was extended, there are still too many school leaders that have been unable to find qualified substitutes for Monday.”

Mayor de Blasio and schools Chancellor Meisha Porter have both asserted that ample auxiliary staffers can address staffing needs as they arise.

“There are support systems in place to ensure schools have the staff they need to take care of their students including 9,000 vaccinated substitute teachers, 5,000 vaccinated substitute paraprofessionals, qualified Central staff who can be redeployed and a new flexible funding allocation for schools to hire additional employees,” the DOE said Friday.

The agency said it was incentivizing substitute applicants with additional pay.

Meanwhile, the city’s public hospital system, the Health and Hospitals Corporation, reported Friday that 93 percent of all of its 46,000-strong staff have received at least one shot, so far.

Like de Blasio’s order for the DOE, Gov. Kathy Hochul ordered all hospital and nursing home employees across the state to get their first shots to continue working — and set a Sept. 27 deadline.

Hizzoner said Friday that all of H&H’s hospitals remain fully functional after the mandate kicked in, though some upstate facilities have reported staff shortages and curtailed services.

The other 300,000 municipal workers in the Big Apple are covered by de Blasio’s test-or-vaccination policy, which requires employees to get their shots or face weekly swabbings for COVID-19.

The vaccination rates at those agencies have surged too in recent weeks, following the new testing regime and passport requirements that require proof of vaccination to enjoy indoor dining or entertainment.

New figures provided by City Hall late Friday show that overall now 80 percent of the city workforce has gotten at least one shot, including:

However, vaccination rates continue to lag among firefighters and jailers.

Just 59 percent of the FDNY’s firefighting staff has been vaccinated — up just 4 points over the last two months.

And the Department of Correction remains the least vaccinated of the entire workforce, with only 49 percent of employees having received at least one shot. That’s up 12 percentage points from 37 percent.