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    In civil action, feds seeks new penalties for New Bedford fishing mogul

    Carlos Rafael in 2014.
    John Sladewski /Standard Times via Associated Press
    Carlos Rafael in 2014.

    Federal authorities aren’t done with “The Codfather.”

    The National Oceanic and Atmospheric Administration this week issued a civil enforcement action against New Bedford fishing magnate Carlos Rafael, seeking to revoke 38 commercial fishing permits and impose a nearly $1 million fine, an official said Friday.

    Regulators also want to rescind operator permits issued to two of Rafael’s scallop vessel captains and deny Rafael any future fishing permits.

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    Rafael and other targets of the enforcement action have 30 days to request a hearing before an administrative law judge, said NOAA spokeswoman Jennie Lyons.

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    In September, Rafael was sentenced to nearly four years in prison for tax evasion and circumventing fishing quotas by falsely labeling more than 700,000 pounds of fish. Rafael misreported cod as less valuable fish, allowing him to boost his profits but hurting small fishermen who followed the law.

    Rafael, who became known as “The Codfather” for his brash business style, said at his sentencing that he ran the illicit enterprise to protect his workers’ jobs. That drew a rebuke from US District Judge William G. Young, who said Rafael’s actions were “designed to benefit you, to line your pockets.”

    Peter Shelley, senior counsel with the Conservation Law Foundation, welcomed NOAA’s enforcement action, saying regulators were trying to make an example of Rafael.

    “The good news from our perspective is that the agency is showing that it matters that the law is followed,” he said.

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    New Bedford’s mayor, Jon F. Mitchell, said he feared the penalties would hurt “innocent third parties,” from fishermen who worked on Rafael’s vessels to companies that provision ships.

    “Carlos was a scoundrel,” said Mitchell, a former federal prosecutor. “This case is not going to cripple the port of New Bedford, not nearly so, but it will hurt individuals who played no part in the underlying fraud.”

    New Bedford officials have urged federal officials to let Rafael’s fishing permits stay in the city rather than distribute them to fishermen in other parts of the region. A NOAA spokeswoman declined to comment on the fate of the permits, saying the agency could not discuss ongoing litigation.

    Rafael’s lawyer could not be reached for comment.

    Rafael was a prominent figure on New Bedford’s waterfront, where he rose from a teenage immigrant from the Azores who sold fish from the back of a truck to the head of a commercial fishing empire. At one point, he owned 32 fishing vessels and 44 fishing permits, which amounted to one of the largest commercial fishing businesses in the United States.

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    In October, Rafael was ordered to forfeit his interests in four fishing vessels and their associated fishing permits, which were valued at nearly $2.3 million. Prosecutors had asked a federal judge to make Rafael forfeit 13 of his vessels and their permits, which are worth more than $19 million.

    The following month, federal regulators prohibited 60 permit holders, including 22 active vessels, from going back to sea until at least the start of the new fishing season in May. Rafael owned most of the vessels in question.

    Regulators said that the region’s fishery cooperative had “failed its primary responsibility of accurately reporting and tracking its catch and has taken only minimal, insufficient steps to ensure accurate reporting and compliance.”

    Mitchell estimated that the grounding of vessels has cost the city’s businesses about $500,000 a day.

    NOAA regulators are also alleging that “Rafael and related entities” misreported where they caught yellowtail flounder in 2012. As a result, NOAA is seeking to revoke additional permits and levy a $140,000 penalty. NOAA further alleges that Rafael, along with two of his fishing vessel operators, misreported scallop harvests in 2013.

    Danny McDonald can be reached at daniel.mcdonald@globe.com. Follow him on Twitter @Danny__McDonald. John R. Ellement can be reached at ellement@globe.com.