BOSTON – A federal appeals court on Wednesday rejected claims by New England’s two largest fishing ports that federal regulators improperly enacted fishing rules that they say are wiping out local fleets.

The 1st U.S. Circuit Court of Appeals decision upheld a 2011 lower court ruling on a suit brought by the ports of New Bedford and Gloucester, as well as fishermen and fishing groups.

The plaintiffs argued the new rules were installed in 2010 without required safeguards, including a two-thirds referendum by fishermen that could have killed the changes before they were enacted. They asked the appeals court to order the lower court to implement the safeguards, alleging that without them, the industry’s smaller fishing businesses would be squeezed out.

But the three judge panel noted that, rather than destroying smaller business, many believe the new rules provide better protection. And it said federal regulators installed the law properly. “The Secretary (of Commerce’s) judgments here were derived from the record, rational, and not based on any error of law,” the court wrote.

The old fishing management system tried to prevent overfishing mainly by limiting the number of days fishermen could go to sea. The new system allots portions of the catch for each species, such as cod and flounder, to individual fishermen. The fishermen then combine and manage those allotments in groups called sectors.

The ports — with support from U.S. Reps. Barney Frank and John Tierney — alleged that, under federal law, the change should have been subjected to a vote that never occurred. They said that because individual catch shares can be transferred among fishermen, the new system fosters broad industry consolidation, as larger fishing interests buy out fishermen whose catch shares are too paltry to support their business.

New Bedford Mayor Jonathan Mitchell expressed disappointment and said the city will consider whether to appeal.

“The general points we were trying to establish through the lawsuit will continue to be a goal for us here in New Bedford. That goal was to ensure that fisheries’ regulations are fair and take into consideration the interests of the fishing families and the communities they live in,” Mitchell said.

Attorney Stephen Ouellette, who represented the New Hampshire Commercial Fishermen’s Association, also said he was disappointed. He also wasn’t sure if the plaintiffs would pursue another appeal.

He said fears about the new rules have been borne out since they went into effect, with the industry shedding jobs, facing huge cuts in catch for key species and a greater share of that catch in fewer hands.

“The fishery is now available to the highest bidder,” he said.

But advocates of the new system say the industry’s problems are rooted in unhealthy fish populations, not fishing rules. And they argue the new system gives fishermen more options to survive cutbacks, such as by allowing them to chase fish stocks without worrying about using up an ever-shrinking number of days at sea.

Peter Shelley, senior counsel of the Conservation Law Foundation, which intervened on behalf of the government, said the plaintiffs’ claims “bordered on frivolous” and amounted to a “political sideshow.”

He said with two unambiguous court rulings in the government’s favor, there should be no doubt now that the fishing law is legal.

“The challenge now is to get this fishery functioning in the way it ought to be functioning,” Shelley said.