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.
He also called for appropriate disciplinary action for any staff members who knowingly violated protocol or failed to report a lab incident.
The CDC said it learned of the flu mix-up while it was finalising 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.
"There were no exposures as a result of that incident."
The lab is closed until better safety measures can be put in place, and an investigation is under way.
The H5N1 bird flu is highly contagious and has killed about 60 per cent of humans who have been sickened by it.
It first infected humans in 1997 during a poultry outbreak in Hong Kong, and became widespread in 2003 and 2004.