The ruling also highlights the potential for future shifts in federal regulations over animal agriculture practices. Such changes could force beef, pork and poultry producers to buy more grain and find other ways to fatten animals prior to slaughter.
Critics of antibiotics in animal feed called the ruling a victory in an increasingly contentious fight.
Organizations such as the Union of Concerned Scientists and the American Academy of Pediatrics argue that such farming practices endangers people who grow ill from resistant bacteria but cannot be treated with standard antibiotic therapies.
"We want them to evaluate safety and effectiveness (of such practices), and we think that's something the FDA has been avoiding," said Avinash Kar, an attorney for the Natural Resources Defense Council. "We think they've caved into the industry."
The livestock industry was disappointed by Katz's order, and said the use of such medications is necessary to prevent and treat animal health issues.
Industry officials, citing conflicting scientific research, say such practices pose little risk to public health.
"The actual human health risk of the use of antibiotic use in animals resulting in the inability of the drug to treat human disease is extremely small - in one instance, less than the risk of dying from a bee sting," the Animal Health Institute, a trade group that represents pharmaceutical companies, said in a statement on Tuesday.
The agency unveiled voluntary guidelines this past April for both drug manufacturers and livestock producers to curtail the use of antibiotics on farm animals.
But Katz said that these voluntary measures are not a substitute for the FDA reviewing the petitions.
"The Agency must evaluate the safety risks of the petitioned drugs and either make a finding that the drugs are not shown to be safe or provide a reasoned explanation as to why the Agency is refusing to make such a finding," Katz wrote.
The lawsuit seeking to spur the FDA to restrict antibiotic use in animals was filed in 2011 by groups including The Natural Resources Defense Council, Center for Science in the Public Interest and the Union of Concerned Scientists.
The case is Natural Resources Defense Council et al. v. FDA, in the U.S. District Court for the Southern District of New York, No. 11-3562. (Reporting by P.J. Huffstutter and Sakthi Prasad; Editing by Tim Dobbyn)