BOSTON – New England’s largest fishing ports said Wednesday that regulators ignored congressional intent when they instituted fishing rules that the ports complain are crushing local fleets.

An attorney for the ports of Gloucester and New Bedford, along with lawyers for local fishermen and associations, told the 1st U.S. Circuit Court of Appeals that regulators bypassed safeguards in fishery law aimed at protecting smaller fishing businesses from being swallowed by wealthier interests.

“One of the primary concerns is the preservation of the small-business model that we’ve had for 375 years,” said attorney Steve Ouellette, who represented the New Hampshire Commercial Fishermen’s Association in a lawsuit seeking the safeguards.

The ports argued that the court should order a lower court judge to oversee the implementation of the safeguards. That could effectively kill the overhaul because one of the measures requires fishermen to approve the rule changes by a two-thirds vote.

But U.S. Department of Justice attorney Joan Pepin, representing federal fishing regulators, argued that the 2010 rules were properly instituted after months of public debate. The fishing industry’s current struggles far pre-date the new rules, which are intended to help fishermen survive cuts in catch limits that everyone knew were coming because key species are in poor shape, she said.

Fishermen absorbed big cuts this year and face huge cuts next year, including 70 percent reductions in the cod catch. Any court decision won’t affect those cuts.

Peter Shelley, senior counsel of the Conservation Law Foundation, which intervened on behalf of the government, warned the judges that the fishermen represented in the room didn’t speak for how all fishermen feel about the new rules, which he said enjoy broad support.

“No one is in love with the program, but the alternative would be far worse,” he said.

The old system tried to stop overfishing by controlling fishing effort, such as by limiting the number of days that fishermen could go to sea. The new system, installed in May 2010, gives fishermen individual portions of the total catch limit of species such as cod or haddock, and they then pool their allotments in groups called sectors.

Regulators say this gives fishermen more ways to survive the coming cuts. For instance, they can augment their catches by targeting less valuable species because they don’t have to worry about burning up a limited number of days on a relatively low-value fish.

But critics say that because the individual catch shares can be transferred among fishermen, it opens the door for broad consolidation, as larger businesses scarf up the shares of fishermen who got lousy catch allotments.

In June 2011, U.S. District Court Judge Rya Zobel rejected all of the plaintiffs’ arguments against the new sectors system.

On Wednesday, the attorney for the ports, James Kavanaugh, focused on an argument that the judge called a “close call” in her decision — whether the catch allotments given to fishermen amounted to an “individual fishing quota.” He said it was “unambiguous” that they were.

And under the law, he said, that type of quota can’t be installed without the various safeguards to prevent fleet consolidation, such as the fishermen’s referendum and steps to limit any costs.

But Pepin said the allotments aren’t individual fishing quotas because they didn’t give any fishermen an exclusive right to a certain amount of fish. They’re basically used so fishermen know how much catch they bring into a sector, she said.

“It is not an individual quota,” she said. “It’s a piece of data.”

The court gave no timeline for a decision.