"I was hoping to come earlier, but of course couldn't because of school and work," said one person waiting in line. "I just hope they'll offer it again."
The same long lines can be seen across the country and now the CDC says millions will be left out in the cold for weeks. Iowa is waiting on more than 50,000 doses and Colorado is 133,000 short, reports CBS News correspondent Jeff Glor.
"We are seeing more and more vaccine becoming available, we wish it was more than it is, but at least we have some," said Dr. Anne Schuchat with the CDC.
The CDC was hoping to have shipped 40 million doses by the end of October, the reality of having between 28 and 30 million makes for very difficult choices.
Morris County New Jersey's Health Department Chief Peter Summers has a job no one wants - doling out the precious commodity everyone is looking for.
They chose to give their first wave of limited supplies to EMS workers, one of the groups on the CDC's priority list.
The CDC always has known that what has become the biggest public vaccination program in U.S. history would have some growing pains. But Friday's announcement of a shortfall comes at a critical time, when both public anxiety is peaking, and illness levels are rising.
"What we really need to get across to the public is this is going to be tough to have a systematic and rapid access to vaccine right now and they have to prepare for that over the next few weeks, while we're telling them they have to get their immunization," said Dr. Michael Osterholm, an infectious disease expert at the University of Minnesota.
The CDC calls it a "challenging time, "and Friday called for patience.
But with the,story=5389928> deaths of 11 more children this week, the fear is the flu may be arriving faster than the vaccine.
CBS News anchor Katie Couric spoke with CBS News medical correspondent Dr. Jennifer Ashton about the H1N1 Virus.
Couric: Why this sudden news about a shortage? The government had said vaccine production was on track.
Ashton: We spoke to experts today who told us that the projections on availability of H1N1 vaccine were very optimistic all along so in some ways this news is not surprising. Remember this is virus where the first cases were found in late March; so it's been a race all along to get a vaccine ready. Also, there have been production problems with this particular vaccine since the very beginning of the manufacturing process in early June. The viruses for vaccines are grown in eggs for vaccines, some grow very fast - this one never did. Unfortunately there's nothing that can be done to speed up production.
Couric: But what can people do in the meantime if they can't get the vaccine now?
Ashton:: Practice the basics: wash your hands, get plenty of rest, if you're sick stay home. The one thing you should not do is go on the Internet and order drugs that are marketed as treatment for H1N1. This week the government issued a warning about on line selling of unlicensed products - some Tamiflu bought over the internet can be fake.
Couric:: There are. What does that mean? Should we be worried?
Ashton: Not really. This is not unexpected. We know the H1N1 virus has genetic material from pigs. It's possible the pigs got the virus from a person. It does not mean that the virus is mutating. And we need to remind people that you cannot get swine flu from eating pork.