The problems involve Biosafety Level 3 labs at the Centers for Disease Control and Prevention in Atlanta, USA Today reported Tuesday.
The labs are used for experiments involving anthrax, dangerous strains of influenza, the SARS coronavirus and other microbes that could possibly be used as bioweapons.
In February, air from inside a potentially contaminated lab briefly flowed out into a "clean" corridor while a group of visitors who weren't wearing any protective gear were touring the facility, internal CDC e-mails showed.
While the agency said no one had been infected, one expert says the incident represents a major violation of laboratory operating standards.
CDC documents about problems at the labs "raise serious concerns," Rutgers University biosafety expert Richard Ebright said. "There appear to be significant irregularities."
CDC engineers have expressed concerns about the air containment systems since at least 2010, USA Today reported.
The CDC has declined to respond to questions submitted in writing about the problems inside the high-containment labs, the newspaper said.