That message was echoed by Walgreens, one of the nation's largest drugstore suppliers of flu vaccine.
"Due to increased demand for flu shots in recent weeks, select locations may currently be experiencing shortages in supply of flu vaccine," said Robert Elfinger, a company spokesman.
Walgreens is working on ensuring a steady supply and plans to be able to continue offering flu shots through the season.
Sanofi Pasteur, which provides about half of the flu vaccine in the U.S., told NBC News on Thursday that it had sold out of four of its six formulations of its Fluzone seasonal flu vaccine because of late-season demand for vaccines. The company still has other vaccines available for adults and children, officials said.
On Twitter, some flu-wary patrons have been posting their frustrations:
"Heard the flu shot is spreading like never before, had to call 5 places to find the flu shot in stock. I am vaccinated," one shot-seeker wrote.
As of Jan. 4, more than 128 million doses of flu vaccine had been distributed across the country, according to latest CDC figures. That's out of 135 million produced for this season.
There's no word yet on how many people actually have been vaccinated; by the end of November, about 112 million people in the U.S. had received shots, but that number likely has risen sharply.
That's because this year's flu season started early and includes a virus that causes unusually severe illness. Flu has now spread to more than 80 percent of the country, the CDC said.
(Read More: NBC: Are You Worried About Missing Work If You or Your Kids Get the Flu?)
(Read More: NBC: Bad Flu Season Worsens as Boston Declares Emergency)
(Read More: NBC: Who Gave You the Flu? New App, Docs Help Place the Blame)
The agency will issue new figures on Friday, but latest reports indicated that more than 2,200 people had been hospitalized since October and 18 children had died.
This year's flu vaccine is a good match for the circulating viruses, CDC has said. It covers two strains of influenza A and one strain of influenza B. However, a second B strain is not covered and may be accounting for 8 percent to 10 percent of illnesses, infectious disease experts said.
One good way to find flu vaccine nearby is through the HealthMap Vaccine Finder. The site includes some 40,000 locations across the U.S. Users can plug in their addresses or ZIP codes and find which sites are offering vaccine.
There's still time to get the vaccine, which can prevent illness – or at least shorten its duration and severity. It takes two weeks for immunity to build up after the shot, so health officials are encouraging people to take action now.
There's really no shortage of the shots, just some local disruptions in supply, said Erin Fox, manager of the Drug Information Service at the University of Utah, which tracks drug shortages.
"Tons of flu vaccine still available!" Fox says.
