BOSTON — The U.S. Commerce Secretary has ordered nearly $650,000 in unjust fines returned to Northeast fishermen while the National Oceanic and Atmospheric Administration chief apologized to the group and said the move marks a turning point in their tense relationship.

New England fishermen have complained for years of abusive treatment, retaliation and excessive fines by the nation’s fishery law enforcers.

Last year, Secretary Gary Locke appointed special investigator Charles Swartwood after a report by the Commerce Department’s inspector general that flagged several questionable penalties against fishermen.

Swartwood has reviewed 30 cases to date, and on Tuesday Locke said he was returning money to 11 people based on Swartwood’s recommendations.

NOAA chief Jane Lubchenco said with Locke’s decision “we acknowledge and rectify past mistakes.”

“I want to apologize to the fishermen and businesses hurt by these mistakes,” she said in a press call with reporters.

Former scalloper Jim Kendall didn’t get money back in his case, which dated to the 1980s, but said the overall admission of wrongdoing “means more than the money, to be honest with you.”

“It was denied and we were vilified and we were called all kinds of names by people on that side of the fence,” he said.

An attorney for a union that represents fishery enforcement officials noted that Locke found no cause to discipline any officer or attorney, whom he said had been “unfairly tarnished” in the probe.

Richard Hirn of the National Weather Service Employees Organization said when Swartwood interviewed NOAA’s attorneys, he seemed to have already made up his mind about the cases.

“[Swartwood’s] investigation was unfair to the employees because his conclusions were predetermined and politically motivated,” Hirn said.

Fishery enforcement officers ensure fishermen comply with a complex mash of federal regulations, governing everything from where and how they can fish to the gear they can use.

In 2009, Lubchenco ordered a review of the enforcement system by the Commerce Department’s Inspector General, Todd Zinser. His office found abusive treatment of fishermen, though it wasn’t widespread. It also said the process for penalizing violators appeared arbitrary.

Zinser later revealed that former top fisheries cop Dale Jones had wrongly ordered documents shredded during the investigation. He also said the millions in fines paid by fishermen had been used on questionable expenditures, such as a luxury undercover boat and a fleet of vehicles for fishery enforcement officials.

Zinser’s findings sparked Swartwood’s probe, which included interviews with 75 people and review of 100,000 documents.

The bulk of the fines Locke ordered returned come in two cases: $400,000 to former scalloper Lawrence Yucubian, whom Swartwood said was wrongly coerced into paying a large fine, and about $160,000 to Agger Fish Company in Brooklyn, N.Y., which was accused of possessing shark fins without the proper permit.

Locke also canceled tens of thousands in unpaid penalties, including $85,000 charged to the Gloucester Seafood Display Auction, which was accused in 2000 of buying illegally caught cod and faking records to cover it up.

In a statement, the auction said, “We feel vindicated,” but added there should be harsher penalties for the officers who pushed a bogus case that stretched over several years. Jones, for instance, has been removed from his post but still has a federal job.

“The Secretary’s unwillingness to discipline those responsible for these abuses still falls short,” the auction said.

Swartwood is considering another 80 cases brought before him after Locke reversed course in March and allowed him to hear additional cases.

NOAA already has made numerous reforms to its law enforcement division, including tightening controls on the fund that holds fishermen’s fines and putting the onus on NOAA — not fishermen — to prove the fines are fair. Locke said Tuesday that NOAA also would work to make complex rules more understandable and make it clear fishery enforcement exists to serve the fishing community.

Sen. John Kerry said Locke’s decision gave fishermen and regulators a chance to repair their relationship.

“This can be a watershed moment in getting back to a point where people trust each other again in this process,” he said.