The discovery came to light in recent days, and followed concerning reports about mishandled anthrax and forgotten smallpox vials at separate US government labs.
No one was exposed to the mixed flu strain, said CDC director Tom Frieden.
"These events should never have happened," said Frieden at a press briefing.
He said the incidents raise "serious and troubling questions," and added: "Frankly, I'm angry about it."
Frieden said he has issued a moratorium on the transfer of any biological samples, including infectious agents, within or outside the CDC until an investigation is complete.
Also Read
The CDC said it learned of the flu mix-up while it was finalizing a report about what happened with an anthrax incident on June 5, which it concluded was very unlikely to have exposed workers to dangers, though some 80 workers were initially considered vulnerable.
"Earlier this year a culture of non-pathogenic avian influenza was unintentionally cross-contaminated at the CDC influenza laboratory with the highly pathogenic H5N1 strain of influenza and shipped to a BSL-3 select-agent laboratory operated by the United States Department of Agriculture (USDA)," the CDC said in a statement.
The lab is closed until better safety measures can be put in place, and an investigation is under way.
"For me personally, this is the most distressing," said Frieden, who said he learned of it 48 hours ago, though the mix-up happened six weeks ago.
The H5N1 bird flu is highly contagious and has killed about 60 percent of humans who been sickened by it.
It first infected humans in 1997 during a poultry outbreak in Hong Kong, and became widespread in 2003 and 2004.