"We are a bit behind," Dr. Anne Schuchat told CBS' "The Early Show".
Calling the production process "unpredictable," Schuchat said, "We wish we had more vaccine."
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,
The CDC said Tuesday it has a stockpile of close to 13 million vaccine doses, nearly 11 million of which have been ordered by various state governments.
But CBS News correspondent Don Teague reported that some cities across the country - like Dallas - .
CBSNews.com Special Report: H1N1 Virus
Health officials say more than 600,000 people in Dallas County should get vaccinated against H1N1 but only 700 doses have made it to Dallas County's Health Department, Teague reports. Officials are still trying to determine which of the highest risk groups should be vaccinated first.
"This is the time when we have the most flu going on in our community right now, there's a lot of illness right now that could be prevented with the vaccine; unfortunately it's not available yet," said Dallas County Medical Director Dr. John Carlo.
Federal health officials say there isn't actually a shortage of vaccine but it hasn't always made it to the right place at the right time.
Teague reports that in Nampa, Idaho, more than 2,200 doses came in this past weekend and were gone in a day; in southwest Washington State health officials expected 19,000 doses, but are only getting 5,000 this week.
On the other hand, Teague reports, it's more supply than demand in Las Vegas and at one clinic in Miami, they've received significantly more doses than they've given out.
CDC: Learn More About H1N1
CDC: What To Do If You Get Sick
Flu.gov: Where To Get Your Flu Shots