However, on Sunday, many parents say they are being turned away.
With millions of kids home from school, parents figure it would be a perfect time to get a flu shot. Instead, it is turning into a classic case of left hand, right hand.
A spokesperson for one pharmacy chain said the Governor "put the mall in motion without warning." Rite Aid, on the other hand, said they were waiting from the okay from corporate.
CVS says they are hoping to resolve their issues within the next few days, but they stated that their best advice is to call before you go decide to get the vaccine.
Cuomo's emergency declaration comes as the state Health Department reports that the number of patients admitted to hospitals statewide continues to rise with a 55 percent increase in the last week.
Two children have died in New York State so far and at least 10 New York City adults have died from flu-related illness. Statewide adult deaths aren't tracked.
The executive order permits pharmacists to administer flu vaccinations to patients between 6 months and 18 years of age, suspending a section of State Education Law that would normally limit the authority of pharmacists to administer immunizing agents to individuals 18 years of age or older.
Cuomo said he has directed his administration, the New York State Health Department and others to use all resources necessary to deal with the problem and to "remove all barriers to ensure that all New Yorkers - children and adults alike - have access to critically needed flu vaccines."
Flu is widespread in most states this year, and at least 20 children have died.
In declaring the health emergency, the governor cited the worst season for influenza in at least four years with all 57 counties statewide and all five boroughs of Manhattan counting among the 19,128 cases reported so far. That's more than four times the 4,404 positive laboratory tests reported during last year's flu season.
A promotional campaign to encourage anyone who has not gotten a flu shot to get one would be carried out, along with the message that it is not too late to get a shot, the governor said in a release.
Health professionals say the vaccine will prevent about 62 percent of the people who get it from getting the flu while the rest will have a milder case of it. A vaccine takes two weeks to fully kick in.
People can decrease their odds of getting the flu by washing their hands frequently and avoiding touching the eyes, nose and mouth. Because viruses can be spread by the hands as well as the air, health professionals recommend coughing into an elbow rather than the hand and staying home to treat the flu rather than going to work and spreading the illness.
Flu season generally peaks in January and February and can linger through March. This year's severe flu season follows the mildest ever recorded last year.
New Yorkers can find a local vaccine provider by visiting http://flushot.healthmap.org/ and entering their zip code. New Yorkers without internet access can call 1-800-522-5006 or through TTY access at 1-800-655-1789 to find a nearby provider.
Mirroring a wave of illness throughout 47 states, data show incidence of the flu has been widespread throughout New York for seven weeks.
Doctors say flu season started early this season. Nearly 7 percent of all visits to health care providers were flu or flu-like illnesses in the first week of the year, compared with a typical 2 percent, Health Department figures show.
LINK: SUBMIT YOUR QUESTIONS ABOUT THE FLU
"It's a really bad year," said Dr. Ken Steier, a lung specialist and clinical dean at Touro College of Osteopathic Medicine, who estimated he's seeing five times as many cases as is typical for this time of year. "It's really been knocking people out."
And it's likely to spread more, said Dr. Paul Hamlin, a pulmonary disease specialist based on Long Island. "I would expect to see more of it in the next four weeks," he said.
Typically, cases peak and then taper off, but it's hard to predict if this is a normal cycle or the outbreak will last through late March, when the seasonal illness usually falls off.
One reason for that is that the flu is highly contagious. An uncovered sneeze in a crowded subway car or a sick colleague who refuses to stay home from work can spread the illness quickly.
"The risk of getting the flu is definitely increased when you're in close contact with strangers," said Steier. And even those who stay home until they feel better can spread the virus, he added. "You're actually still contagious after you feel better."
Steier said the incubation period - the time between first exposure and when symptoms develop - can be up to seven days. The worst symptoms usually pass in a few days, but it's still possible to pass it along up to 14 days later.
Many people can treat their symptoms with rest, chicken soup or other fluids, and aspirin or Tylenol. But those with severe symptoms should contact their doctors.
Kate Allan, 16, said three days of exhaustion and achiness drove her to visit an Urgent Care facility in Manhattan on Friday, despite the fact that she has had a flu shot.
"My mom said it might not be the flu but my dad is really sick and my brother just had the flu, but he didn't have a flu shot," she said. "We weren't really sure what it is so we came in here today."
Allan's flu test came back negative, so Dr. Neal Shipley sent her home with Tylenol.
"The flu doesn't care if you're a man or a woman, old or young. It just wants to know if you've been vaccinated or not," he said.
Emergency room visits for the flu have jumped along with reported cases overall. Dr. Dan Wiener, the chairman of emergency medicine at Saint Luke's Roosevelt Hospital, said the increase is stressing capacity at the Manhattan hospital, which like several other facilities was already taking on a greater role to compensate for hospitals closed or damaged by Superstorm Sandy.
But Wiener said it makes sense to stay out of the emergency room unless you're in a high risk group, like the elderly, or experiencing very serious symptoms like a persistent high fever. "Unless you're in a high risk group, there's not much we can do," he said.
Still, it's a serious illness. The flu has killed two children in the state already this season, and 20 have died nationally. At least 10 residents of long-term care facilities like nursing homes have died in New York City's five boroughs. City nursing homes are seeing an epidemic, Wiener said, noting that people who are already ill or weak before contracting the flu are more vulnerable.
Hospitals are trying to separate patients who appear to have the flu in emergency rooms and if they're admitted, but so far none in New York appear to be taking the drastic step of screening visitors, which has been reported in Boston, where Mayor Thomas Menino declared a public health emergency due to the flu on Wednesday.
Doctors have mixed opinions about whether this year's flu is more severe than past years, or if it just spread faster. But all agree that for those who haven't been sick yet, it makes sense to get a flu vaccine. Each year's vaccine is designed to combat a different strain of the virus, and this year's shot was successful in targeting the most prevalent strain.
The vaccine will help about 70 percent of people who get it avoid the illness altogether, and the remaining 30 percent will likely have a milder case.
And Steier said don't worry about getting the flu from the shot itself. "That's not possible," he said. "It's basically a killed virus."
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Get more information about the flu from the Centers for Disease Control at CDC.gov.
