Updated

A divided federal appeals court on Thursday upheld a U.S. Food and Drug Administration policy allowing the use of various antibiotics in animal feed, even if such use might endanger the public health.

Reversing a lower court ruling, the 2nd U.S. Circuit Court of Appeals in New York said the FDA was empowered to reject two citizen challenges to its policy, which discourages but does not ban the use of penicillin and some tetracyclines in feed for chickens, cows and pigs, even if they are not sick.

Critics and some scientists say the prolonged, widespread use of the feed to promote weight gain in animals can foster "superbugs," exposing humans who contact or eat the animals to antibiotic-resistant bacteria. They said the FDA should have followed through on its 1977 proposal to ban the feed entirely.

The FDA has long since promoted voluntary limits on animal feed containing the antibiotics. In December it began implementing a plan to phase out the feed's indiscriminate use, with an exception for when such use is "medically necessary."

In 2012, U.S. Magistrate Judge Theodore Katz in Manhattan agreed with the Natural Resources Defense Council (NRDC), Public Citizen and other groups challenging the FDA policy that the refusal to consider the citizen petitions, which date from 1999 and 2005, was arbitrary and capricious.

Writing for a 2-1 appeals court majority, however, Circuit Judge Gerard Lynch said the FDA deserved deference, even if agency officials had scientific concern about the feed's safety.

"While the agency regards the indiscriminate and extensive use of such drugs in animal feed as threatening, it does not necessarily believe that the administration of antibiotics to animals in their feed is inherently dangerous to human health," Lynch wrote.

As a result, he said the FDA was not arbitrary or capricious in denying the petitions, or in encouraging what the agency has called "judicious" use of the feed, rather than seeking to withdraw approval through a "protracted administrative process and likely litigation."

Chief Judge Robert Katzmann dissented. He said the decision lets the FDA "openly declare that a particular animal drug is unsafe, but then refuse to withdraw approval," and "effectively ignore" challenges to that policy. "I do not believe the statutory scheme can be read to permit those results."

Jennifer Sorenson, a lawyer for the NRDC, said the decision "effectively gives the FDA a free pass to ignore the science when it is politically inconvenient." She said the group will explore its legal options.

FDA spokeswoman Jennifer Dooren said, "The FDA is currently reviewing the decision but is pleased with the outcome."

On June 30, the FDA said all 26 drugmakers affected by its December plan had agreed to "fully engage in" phasing out the use of the antibiotics in animal feed for food production, and phasing in veterinarians to oversee the remaining medical uses.

The case is Natural Resources Defense Council Inc et al v. FDA et al, 2nd U.S. Circuit Court of Appeals, Nos. 12-2106, 12-3607.