"The FDA is supposed to protect public health, but they are falling short," said Carmen Cordova, a microbiologist for the Natural Resources Defense Council and the study's lead author.
The NRDC looked at records from 2001 to 2010 (secured through the Freedom of Information Act) and found that the FDA's internal scientific reviews of 30 drugs used in livestock concluded that the drugs likely exposed humans to antibiotic-resistant bacteria through the food supply, the study says.
(Read more: A 'superbug' fix? Agribusiness doesn't think so)
At least nine of the 30 antibiotics potentially harmful to humans are still being used in animals, according to the council.
"That's a breach of their responsibility and to the public trust," Cordova argued.
While not responding directly to the NRDC's contention that drugs harmful to humans are being used in animals, the FDA defended its research methods for antibiotic use in livestock.
In a response to CNBC, the FDA said that based on its "review of this [safety data on antibiotics from producers] and other information, the agency chose to employ a strategy that would more broadly address the concerns about the production use of medically important antimicrobials in food-producing animals."
It added that "our strategy also does not limit our authority to take future regulatory action."