The pop-up vaccination sites are located at 180th Street in the Bronx and the Broadway junction station in Brooklyn.
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Both open at 8 a.m. Wednesday.
This comes as MTA officers descended on rush hour commuters in Penn Station Tuesday.
They will be doing more of that today at subway stations across the city.
They are handing out free masks, and anyone who refuses to wear one will get a $50 ticket.
Compliance has slipped below 90% in recent weeks, and officials are hoping to reverse that trend.
Exclusive: MTA police enforce mask mandate in Penn Station
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The mask mandate applies across the board, in subways and on commuter rail lines.
Masks are not required in open-air, above-ground stations.
"We put a lot of effort into trying to get them to realize it's still a rule, it's a law," said MTA Chief Safety Officer Patrick Warren. "And it's for their own health and the health of everyone around them."
Riders aren't thrilled about it, but realize they have little choice.
LIRR commuter Craig West only had to be told once.
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"And I had to wear it. And I'm not happy about wearing it, but it's not the biggest deal in the world, you know?" West said.
Over the past last year, MTA police have only handed out about a dozen tickets. That may change in the coming days.
But officials say this is really not about tickets or fines, but getting people to mask up.
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