Health officials nationwide are urging healthy adults and schoolchildren to skip the shot, after for the U.S.
With 46 million doses now unavailable, the government says the 54 million flu shots left from a rival firm should be reserved for youngsters ages 6-23 months, people 65 or older, anyone living with babies younger than 6 months and others in high-risk groups.
Some state health officials are now watching for price gouging.
Barbara Ertle, the pharmacy director at Saint Joseph Medical Center in Towson, Md., says some wholesalers are charging exorbitant prices for flu vaccines, as much as $650 for 10 shots.
"You need to pay a bit of a premium, but 'a bit of a premium' is not 60 times the price," she told CBS Radio News. You have to say, 'where is a legitimate profit and where is this price-gouging?'"
St. Joseph has no flu vaccine at all, Ertle reports. The shutdown of flu vaccine production at Chiron Corp. has slashed supplies across the nation. Public health clinics in Georgia and Pennsylvania will lose nearly a third of their doses. Minnesota canceled flu clinics for state employees and set aside vaccines for those at high risk.
The news carries particular concern in Colorado, which was the epicenter of last year's flu season with 12,885 reported cases and the deaths of 12 children.
Josh Duignan got his first flu shot last year when his wife was pregnant with their first child. While son Ethan will get a shot this year, Duignan isn't sure whether he'll also get a chance to roll up his sleeve.
Duignan, in Colorado, knows his pediatrician has enough doses to vaccinate Ethan, now 7 months, but isn't sure whether he will get a shot.
"If they turn me down, I don't know what I'll do," he said. "But I'm going to get one this year. I promised my wife I would."
Those who can't get the shots still have alternatives, says The Early Show's Dr. Emily Senay.
There are three antiviral medications on the market that can be used for people who come in contact with the flu to prevent them from getting it. These are prescription medications, and while not everyone can take them, she expects them to be used more widely than in the past.
But Senay says good hygiene is still the best non-vaccine preventative.
"I can't say enough about hand washing again and again," she said. "Studies show that hand washing will dramatically reduce your risk of getting all sorts of things, not just the flu, but gastrointestinal illness and colds."
Another possibility is hand sanitizers.
"Those work, too. Throw one of those in your pocket and take it with you.
"You have to remember the flu virus can live on surfaces for hours so if you touch a door knob that someone has just passed through, you want to avoid putting your hands on your face and your nose to reduce your risk of transmitting it to yourself," she added.
Doctors at Arvada Pediatric Associates in suburban Denver normally recommend flu shots for siblings of children with asthma and other risky conditions. But even those children are expected to forgo shots this year, president Charyl LeBlanc said as the office fielded calls from panicked parents.
"It's been a wild day," LeBlanc said Wednesday. "Part of the problem is everybody is remembering the flu season last year, particularly in Colorado."
"It's kind of disappointing that we didn't have more than two sources to get the vaccine," complained Dan Knuth, 59, of New Brighton, Minn., who said he probably won't get a shot this year. "It shows the vulnerability of our health care system."
"Worst-case scenario, we will have probably more patients being hospitalized with pneumonia," said Dr. Wellington Liu, medical director of Kateri Medical Residence in New York City, a nursing home with 440 long-term patients.
With a 7-month-old baby, Barbara Askenazi said she planned to call her pediatrician to see whether her she and her 2½-year-old son Buddy, who mixes with plenty of children at nursery school, should get shots anyway.
"It just dumbfounds me that they can't figure out how to make enough," said Askenazi, 36. "People know the flu is coming, they know how dangerous it is, but there's always a shortage of vaccine."
The vaccine shortage will also have economic impacts. The Minnesota Visiting Nurse Agency counts on proceeds from its flu clinics to help fund some 80,000 home visits a year. It expected to receive 150,000 doses this year from Chiron.
"We had to cancel everything," said Mary Ann Blade, the agency's chief executive.