Thousands of appointments have been cancelled, and now questions are being asked about those second doses.
So far about half a million New Yorkers have gotten their vaccine.
The vaccine mega-site at the Brooklyn Army Terminal has reopened after closing for several days.
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But with 97 percent of the state's vaccine supply now exhausted, both the city and the state are on pace to run out of vaccines.
At a Friday briefing, Gov. Cuomo said the state would run out of the allocations it has received so far by the end of the day.
Cuomo said deliveries of the week six allocations, about 250,400 doses, had begun, but those deliveries "are delivered by the federal government by various means and they arrive at different times throughout the week."
The state is able to administer about 80,000 doses per day and could easily do 100,000 per day, Cuomo said.
"The moment the vaccines arrive, our goal is to get them in arms as soon as possible. 250,400 doses per week is not enough," Cuomo said.
There are 300,000 shots waiting in storage for second doses.
The city is now considering giving them as first doses for those still waiting and backfilling the supply and delaying by a few weeks the second shot for those who already gotten the first.
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Due to the shortage, city locations have already canceled or postponed 23,000 appointments.
Fifteen vaccine hubs citywide will remain closed until Sunday.
NYC Health + Hospitals facilities are rescheduling all first dose vaccine appointments through Monday, January 25.
The Brooklyn Army Terminal, one the city's five 24-hour facilities, has reopened with limited appointments after it closed for several days earlier in the week.
Meanwhile, Mt. Sinai, after canceling their appointments through Tuesday due to supply constraints, says they resumed vaccine appointments this week on Wednesday, Thursday, and Friday, after receiving a new shipment on Sunday.
However they say the supply issue remains "a complex and fluid situation," and their foreseeable outlook does not stretch far past Friday.
Northwell is in the same boat, saying they are not cancelling and have not stopped booking new appointments, but their supply (for first dose) is "very limited" and they are booking appointments "sporadically" as more supply arrives at their facilities.
NYU Langone is still not scheduling any new appointments due to ongoing supply constraints.
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Meantime, the city's teachers' union is now warning that vaccine shortages could delay the opening of New York City schools in September.
"Increased availability of the vaccine is the key to fully re-opening everything, from schools to businesses," United Federation of Teachers President Michael Mulgrew said in a statement.
As of right now, the plan is to reopen schools with widespread vaccinations.
Teachers are currently eligible to get the shot, but many are finding it hard to get an appointment.
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