"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.
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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."
U.S. livestock have been given antibiotics for more than 60 years. In fact, 80 percent of the antibiotics used in the U.S. go to livestock.
The FDA approved such use in the 1950s, after studies showed that animals receiving antibiotics in their feed gained weight faster than those that didn't get them. That helped cut farmers' production costs.
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In the 1970s, a study found that overusing antibiotics in animals contributed to the creation of drug-resistant bacteria in humans. The FDA issued a ban on nonmedical use of penicillin and tetracycline in animals but has never fully enforced it.
Though the agency has initiated new rules aimed at limiting antibiotic use in animals for production growth, they are voluntary and involve drugmakers' removing such labels.
Some see widespread use of antibiotics in livestock as a preventative health measure.
"The use of growth promotion is being phased out, but keeping animals from getting sick is judicious," said Kelli Ludlum, director of congressional relations for the American Farm Bureau Foundation, an agriculture advocacy group.
According to the Centers for Disease Control, at least 2 million people in the U.S. become infected with antibiotic-resistant bacteria every year, with about 23,000 dying as a direct result of those infections.
Studies estimate that antibiotic resistance accounts for $20 billion in direct health-care costs and $35 billion in lost productivity annually.
The CDC agrees that the overuse of antibiotics in animals is helping to create drug-resistant bacteria that can be transferred to humans.
But not everyone is convinced.
"We're not saying it's not possible that the antibiotics used in animals hurt humans, but at the same time we think the chances of that happening are slim," said Ludlum at the AFBF. "Someone is more likely to die from a bee sting than a treatment failure that can be linked back to antibiotic use in animals."
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But a new study by a team from the University of Iowa, Iowa City Veterans Affairs and Kent State University could provide more support for establishing a link between antibiotic use in animals and human disease.
Released this month, the study says that Iowa residents living within one mile of a pig megafarm—housing at least 2,500 pigs—had nearly three times the risk of contracting MRSA as those living farther away.
MRSA is one of the superbacteria deemed highly resistant to antibiotics. The U.S. sees an estimated 90,000 MRSA infections each year, which result in about 20,000 deaths.
"We can't ignore this problem of overusing antibiotics," said the Cordova at the NRDC. "If we do, we do so at our own risk."
—By CNBC's Mark Koba. Follow him on Twitter