That's because the bacteria the antibiotics are supposed to kill can become resistant to the drugs.
"The resistance is in bacteria associated with the meat and these resistant bacteria can come into us when we eat the meat," says Dr. Stewart Levy.
The system may soon change, reports CBS News Correspondent Diana Olick. The Food and Drug Administration is revising its guidelines for the approval of new antibiotics and reassessing how current ones are used in livestock.
"The point is that, whenever we use antibiotics, we help propagate forms of bacteria that are resistant to antibiotics we want to use to treat people," says Dr. Levy.
Animals consume more than 40 percent of the antibiotics in the US - drugs like penicillin, tetracycline and new drugs used in the fight against salmonella.
Some in the agriculture industry argue the FDA is over-reacting and threatening food safety.
"Herds and flocks of poultry will be less healthy," claims Dr. Richard Carnevale of the Animal Health Institute. "That will lead to more losses for the producer as well as less healthy animals going into the food supply."
The FDA is not going as far as the European Union, which banned the use of antibiotics in animals outright.
Instead, scientists in the US are working on new types of drugs, which could take a decade to develop.