"I don't usually lose sleep despite the many threats we face," Tom Frieden told CBS News. "But I'm losing sleep."
The shutdown means the CDC will no longer be able to produce the weekly national map that tracks flu outbreaks state by state.
The CDC says without cross-state consultation, it simply won't know what's happening with flu.
"Where is it spreading? What types of flu are spreading? Should we be using one medication or another?" said Frieden.
In Idaho, state health officials say it's business as usual, even though the CDC's financial hands are tied, at least for now.
"In terms of our operations and our ability to monitor the flu, we're on top of it," said Niki Forbing-Orr, spokeswoman for the Idaho Department of Health and Welfare. "And we'll stay on top of it."
But CDC administrators worry about other outbreaks they will not be able to monitor, including hepatitis a, salmonella and measles.
They say the shutdown is interfering with the ability to protect people.
Analysts says the shutdown is not expected to affect this year's supply of flu vaccine.
But depending on how long the shutdown lasts, they say a lack of nationwide tracking data could have implications for the development of next year's flu vaccine.