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Carlos A. Rafael, the disgraced New Bedford fishing mogul known as “The Codfather,” has been permanently banned from the commercial fishing industry and fined $3 million under the terms of a civil settlement with federal regulators.

The agreement with the National Oceanic and Atmospheric Administration resolves “pending civil administrative claims” against Rafael, 67, and a number of his former captains, regulators said Monday. Rafael, who had owned one of the nation’s largest groundfish fishing fleets before his downfall, pleaded guilty in March 2017 to perpetrating a massive fishing fraud and was sentenced to 46 months in prison.

Chris Oliver, assistant administrator for NOAA Fisheries, said the settlement achieves the agency’s “chief objective of permanently removing Mr. Rafael from participation in federal fisheries.”

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“The settlement also clears the way for Mr. Rafael’s fishing assets that have been tied up in this litigation to be returned to productive use,” he said in a statement. “It also serves as a reminder that no one is exempt from the rules.”

Rafael must relinquish the seafood dealer permit issued to Carlos Seafood by September 1 and sell “all limited access federal fishing permits and fishing vessels he owns or controls by the end of 2020,” the agency said.

John Markey, a lawyer for Rafael, said both sides had to compromise to reach the agreement.

“The big sacrifice for Carlos is that he’s being asked to no longer participate in the fishing industry, which has been his life, where he has made his friendships, earned his living. This is who he is. It’s where he went every day for work. It’s where he’s met great success and provided for his family,” he said. “It’s like David Ortiz or Joe DiMaggio retiring. He’s not leaving because he aged out, he’s leaving because of this situation. That’s the downside.”

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At his sentencing, Rafael said he mislabeled more than 700,000 pounds of fish not out of greed, but to protect workers whose jobs were threatened by limits on dwindling cod stocks. Prosecutors said he evaded federal limits by falsely reporting cod as less valuable fish, hurting small fishermen who followed the law.

Rafael must sell all his fishing vessels and permits and is allowed to retain the proceeds, regulators said.

“The great majority of Rafael’s civil and criminal violations involved the groundfish fishery; Rafael’s highly valued scallop permits were not used in those violations,” NOAA said.

Markey said Rafael won’t sell his fleet to family members and hopes to keep the boats in New Bedford. The boats include 11 scallop boats and 15 to 20 groundfish vessels, Markey said.

Under the settlement, 17 of Rafael’s former captains had their operator permits suspended. Suspensions range from 20 to 200 days and are based on the number and severity of violations, regulators said.

“This settlement also holds accountable the vessel captains who now face suspensions, probationary periods, additional monitoring and reporting requirements, and the threat of a lifetime ban from the industry if they intentionally violate federal fisheries regulations again,” Oliver said.

New Bedford Mayor Jon Mitchell said the settlement allows the city to “turn the page” on the Rafael saga.

“The most significant element of the agreement is what we have insisted on all along; that is, it imposes no restrictions on Rafael’s ability to sell his boats and permits to New Bedford-based businesses,” he said. “If Rafael follows through on his intention to do just that, it will ensure that East Coast groundfish landings will continue to be concentrated in New Bedford.”

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Authorities say they uncovered Rafael’s scheme when he began talking about it to two Russian gangsters expressing interest in buying his company. The two men were actually undercover Internal Revenue Service agents.


Maria Cramer of the Globe staff contributed to this report. Travis Andersen can be reached at travis.andersen@globe.com. Follow him on Twitter @TAGlobe.