The latest news followed admissions of mishandled anthrax and forgotten smallpox vials at separate US government labs, and raised new concerns about the safety of dangerous agents which could be used as bioterror weapons.
No one was endangered by the mixed flu strain, said Centers for Disease Control and Prevention director Tom Frieden, who nevertheless said he was "astonished" that protocols could have been violated in that way.
"Everything we have looked at strongly suggests that there was no exposure of anyone to influenza," said Frieden at a press briefing.
He told reporters he had lost sleep since learning of the flu mix-up on Wednesday, six weeks after it occurred.
"These events should never have happened," he said, adding that they raise "serious and troubling questions.
"Frankly, I'm angry about it," he said.
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.
"It tells me we need to look at our culture of safety throughout all our laboratories," Frieden said.
- Anthrax, smallpox incidents -
The CDC said it learned of the flu mix-up while it was finalizing a report about what happened with a separate incident involving anthrax on June 5, which it concluded was very unlikely to have exposed workers to dangers, though some 80 people 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 of the flu incident, which took place on May 23.
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.
Frieden said the type of H5N1 was not the exact same type as the one that spread in China, but "it is one of the ones that does concern us because it can be quite deadly both for poultry and for people."
The other type of flu involved was H9N2, he said.
The incidents may raise further concerns among opponents of studies known as "gain of function" research, in which scientists manipulate flu strains to find out how they can more easily spread, as well as how to better vaccinate against them.
In 2011 and 2012, worldwide scientists self-imposed a moratorium on such research after concerns were raised about research that made a potent flu strain jump easily between mammals.
The full details of those experiments were eventually published in leading scientific journals.
- 'Disturbing, scary' -
"It's disturbing. It's a little scary," said Len Horovitz, a pulmonary specialist and internist at Lenox Hill Hospital in New York, regarding the latest CDC revelations.
"The CDC has to have more control of its labs," he added. "More oversight is needed."
The CDC has also completed initial testing on the six apparently forgotten vials of smallpox that were found in a Food and Drug Administration lab at the National Institutes of Health earlier this week, and two had viable smallpox in them, Frieden said.
After scientists complete tests on the smallpox, they will destroy the samples in view of World Health Organization officials, he said.
"That is what should have been done a couple of decades ago," Frieden said.
"Whoever created these vials did not do so out of malice," he said, adding that they were dated February 10, 1954.
Smallpox was not eradicated worldwide until the late 1970s.