The DOT cited concerns about fires caused by the batteries as the reason behind the ban.
Passengers can still check baggage with lithium batteries if they are installed in electronic devices, such as cameras, cell phones and laptop computers. If they are packed in plastic bags, batteries may be in carry-on baggage, but there is a limit is two batteries per passenger.
The ban affects shipments of nonrechargeable lithium batteries, such as those made by Energizer Holdings Inc. and Procter & Gamble Co.'s Duracell brand.
"Doing something as simple as keeping a spare battery in its original retail packaging or a plastic ziplock bag will prevent unintentional short-circuiting and fires," Krista Edwards, deputy administrator of the Pipeline and Hazardous Materials Safety Administration, said in a release.
The Federal Aviation Administration has found that fire-protection systems in the cargo hold of passenger planes can't put out fires sparked in lithium batteries.
The National Transportation Safety Board earlier this month said it could not rule out lithium batteries as the source of a cargo plane fire last year at Philadelphia International Airport.