A federal court has ordered the Food and Drug Administration to revisit its decision not to ban the use of certain antibiotics in animal feed and criticized the agency for relying on industry to voluntarily limit the use of these drugs.

This week, the federal district court in Manhattan ruled that the FDA must reconsider two citizen petitions that asked the agency to withdraw approval of some antibiotics used in food-producing animals. The agency’s denial of both petitions years ago was “arbitrary and capricious,” the court said.

In March, in a decision tied to the same case, the court ordered the FDA to follow through on a proposal it made decades ago that would have banned the use of penicillin and two forms of tetracycline in animal feed.

The back-to-back rulings mark a victory for the Natural Resources Defense Council and the other health and consumer advocacy groups that sued the government. The groups say they expect the FDA to fight back, and the agency already has appealed the March decision. But they also describe this round of the legal battle as a turning point in a decades-long conflict with the agency regarding a major public health threat.

“The FDA has just been dragging its heels, and until now nobody has directed the agency to do something other than what it’s been doing,” said Avinash Kar, a lawyer at the Natural Resources Defense Council.

The concern is that some antibiotics that treat illnesses in people are widely used on livestock to promote disease prevention and weight gain and to compensate for crowded conditions on ranches and farms. The antibiotics are mixed into animal feed at low levels for such long periods that they are likely to breed drug-resistant “superbugs” that can spread to humans who work with or eat the animals, studies show.

In this week’s ruling, Judge Theodore H. Katz said that the agency has recognized for more than three decades that the use of some antibiotics poses health risks for humans but that it has done “shockingly little” about it.

When the FDA rejected the two citizen petitions — filed in 1999 and 2005 — it failed to weigh scientific evidence as required by law, Katz wrote. Instead, the agency considered only the time and cost it would take to withdraw the drug approvals and the fact that it was pursuing alternative regulatory proposals.

Although the two petitions generated 3,000 pages of court filings that contained numerous scientific studies, “the agency did not address or even mention the scientific evidence in its response,” Katz wrote.

The FDA declined to comment on this week’s ruling or the one before it.

For years, the FDA has been pushing a plan that would seek voluntary limits on antibiotics in animal feed. In April, the agency finalized the plan and asked drugmakers to stop using 200 products for growth promotion in animals. Companies that opt to do so will be required to revise their product labels to reflect the change over the next several years.

Once the drugs were relabeled, those antibiotics would no longer be available to farmers over the counter. A veterinarian would have to prescribe them.

The agency said the voluntary path — supported by many in the drug industry — would be much faster than formally withdrawing each drug from the market, a process that would probably result in lengthy administrative proceedings and possibly litigation.

The Animal Health Institute, which represents companies that produce veterinary medicines, said the court’s recent rulings add confusion to the FDA’s voluntary effort. The public would be better served by an orderly transition that phases out the antibiotics and avoids unintended consequences, said Ron Phillips, one of the group’s vice presidents.

On that front, the judge disagreed. Katz said the FDA has failed to explain why its voluntary approach would be more effective than a formal ban.

“However, if any credence is to be given to the agency’s position that the drug industry intends to comply with the voluntary program,” Katz said, “then it is unclear why the industry would contest formal withdrawal notices or require time consuming hearings.”