NEW YORK — New York City’s health department has closed 12 of its 15 neighborhood COVID-19 vaccine distribution hubs for three days, citing a lack of vaccine supply, leaving several neighborhoods that have been hit hard by the coronavirus without immunization sites. 

This is at least the second week that the city had planned to close down most of its vaccine distribution sites Monday through Wednesday after running out of a weekly allotment of vaccines over the weekend, a health department spokesperson said. 

The three open sites are only giving out second dose shots, the spokesperson said, because those locations were the only ones open about a month ago, when residents got their first vaccine doses there. Three other large hubs — 125 Worth Street, in lower Manhattan; the Corona Clinic, in Queens; and the Uptown Clinic in East Harlem — remain open seven days a week.

Volunteers with the city’s volunteer Medical Reserve Corps, who are helping with the vaccine effort, were notified Friday that the sites would be closed in the beginning of the week, according to emails shared with NY1. The email specified that the shifts were cancelled “due to another vaccine shortage.”

Patrick Gallahue, the health department spokesperson, said that the shortage was due to low supply to city-run vaccine sites. 

“We review operations on a regular basis to match staffing needs with supply so that we can vaccinate New Yorkers,” Gallahue said in an emailed statement.

All 15 sites will reopen Thursday, after the city’s vaccine supply is replenished, the spokesperson said, and will be open to people who have made appointments. 

Several of the temporarily closed sites, run by the city’s Department of Health and Mental Hygiene, are in areas with no other vaccine distribution points, according to a city map of vaccine sites.

Those areas have been among the hardest hit by the coronavirus. Aviation High School, in Queens, closed until Thursday, is the only vaccine distribution site for Sunnyside and Woodside, which have had high rates of COVID-19 cases and deaths. Beach Channel Educational Campus, another temporarily closed site, is one of two vaccine centers in the Rockaways, an area with high COVID-19 positivity rates. Canarsie High School, also temporarily closed, is the only vaccine site in Canarsie, home to 100,000 people. 

The sites were open on Sunday, but shut down Monday without any more vaccines to offer. 

“We’ve been in a pattern of extreme supply shortage for weeks now,” said City Councilmember Mark Levine.  “That has particularly impacted city-run sites.”

“It’s a huge problem,” Levine said, since the city-run sites “are exclusively for city residents, and also tend to be located in communities of color.”

The three sites that are open — though only for second-dose vaccine shots — are Hillcrest High School, in Jamaica, Queens; Bushwick Educational Campus, in Brooklyn; and South Bronx Educational Campus. 

The city has been relying on weekly shipments of vaccines from the federal government and the state, with stock dwindling before being resupplied primarily on Tuesday evenings and Wednesdays. As of Tuesday morning, the city had fewer than 43,000 first doses on hand, and about five times that amount of vaccine doses reserved for second shots, which must be taken several weeks after the initial vaccine dose. 

“The capacity to distribute vaccines is much greater than our supply,” Gallahue, the health department spokesperson, said.

Mayor Bill de Blasio has repeatedly called on the state and federal government to allow the city to use vaccine doses reserved for second shots as first shots. New York State Health Commissioner Dr. Howard Zucker rejected a formal request from de Blasio to do so last week. 

At a Monday morning press conference, de Blasio said he was still a “firm believer” in opening up all available doses for first vaccine appointments, since the federal government has indicated they are ramping up production on vaccines.

“We have assurances that are believable, that are tangible, that we’ll have more and more supply,” de Blasio said. 

The temporary closures of the health department-run sites come as the city is opening two large vaccine hubs: at Yankee Stadium in the Bronx, which opened Friday, and at Citi Field in Queens, which opens Wednesday. The sites are aimed at residents of each borough respectively, which have seen the highest impact from the coronavirus in the city,

“We do need to keep making moves that will encourage equity and address disparity, but it’s all against the background of fundamental lack of supply,” de Blasio said Tuesday at a press conference.

The city has vaccinated just over a million people in about seven weeks as of Tuesday morning.

Yet demand for the vaccine is expected to rise dramatically soon, as people with certain health conditions that are associated with higher risk of severe bouts of COVID-19 become eligible for the vaccine next week. 

Levine said the new rules will make about a million more New Yorkers eligible for the vaccine.