City health officials acknowledged the frustration over the restricted supply of the jab and pledged to build a "stable appointment infrastructure" as the supply increases.
Infections now surpass 1,000 from the growing outbreak in the U.S. Most patients experience just fever, body aches, chills and fatigue.
People with more severe illness may develop a rash and lesions on the face and hands that can spread to different parts of the body.
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Vaccine shortages have counted to anxiety around the virus. Health officials say anyone can get monkeypox, yet most cases in the U.S. have been men who have sex with men.
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In San Francisco, where there have been just 68 confirmed cases, residents queued up for blocks to get their jabs.
The Golden Gate City's health department got 2,308 doses from the federal government last week and just 50 remain at the Zukerberg San Francisco General hospital monkeypox clinic, due to their Twitter post.
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They have not set up an appointment website, taking residents on a first come, first serve basis.
They will be forced to turn people away if more doesn't arrive soon, city officials cautioned on Tuesday.
Thus far, health officials have registered that 1,700 doses of the vaccine have been administered.
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"It is extremely infuriating that our federal government has once again failed in their response, especially after a two-year public health crisis," Ande Stone, a senior community manager with the San Francisco AIDS Foundation, explained to the San Francisco Chronicle.
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Scientists caution that anyone who is in close physical contact with someone who has monkeypox or their clothing or bedsheets is at risk of infection, regardless of their sexual orientation.
"After COVID, this should have been easy," announced Daniel Ross, 25, a Harlem man who was one of the many who attempted to make an appointment Tuesday.
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"I kept refreshing and refreshing. ... I was frustrated."
Ross soon gave up on the appointment portal, which went down minutes after it went live.
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"It's going to haunt me," he stated. "Me being a gay man who lives in Harlem, there's a lot of anxiety. I had four mosquito bites, and I was thinking what if this isn't a mosquito bite?"
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The city contracted with the company Affiliated Physicians to run its online appointment service following its previous contractor MedRite also suffered site crashes, according to WNYC/Gothamist.
"This is further proof that demand is very high," the city health commissioner Ashwin Vasan announced in a statement. "We apologize for the frustration caused and are working to build stable appointment infrastructure as we roll out more appointments as vaccine supply increases in the coming weeks."
To date, New York City has administered almost 7,000 vaccinations, while thousands more have been waiting for their chance to get inoculated against the virus.
Health officials stated they were expecting 14,500 doses this week.
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