BOSTON — The U.S. commerce secretary on Thursday ordered a review of several questionable penalties assessed against fishermen in the last decade after a federal report revealed abusive treatment and high-pressure tactics by the nation’s fishery enforcement officers.

Gary Locke on Thursday appointed a special master to examine 19 “problematic” cases in the Northeast that were identified Thursday by his office’s inspector general, Todd Zinser. The special master, retired judge Charles B. Swartwood III, will also look at 104 complaints that weren’t in Zinser’s report.

Zinser’s report detailed a strategy by the law enforcement office to propose large fines in order to prod fishermen toward settling cases. It also cited “animus” toward fishermen by an key attorney handling their cases.

“The problems identified … are unacceptable, were allowed to persist for too long and will end on my watch,” Locke said in a press release.

New Bedford boat owner Carlos Rafael, who said he paid $159,000 for a violation alleging problems with his fishing net, welcomed Locke’s move to re-examine some cases.

“I thought this thing was going to be pushed under the rug,” he said. “But finally, the law works.”

Larry Yacubian, a former New Bedford scalloper, said he was forced out of the industry and paid $430,000 in 2005 after his license was yanked following a disputed charge of fishing in a closed area in 1998. He recalled those years as “torment,” and said Locke’s decision to review the cases, including his, was vindication.

“I feel real good about it,” he said. “But, you know, (the law enforcement agency) ruins people’s lives. … Tony Soprano had more of the milk of human kindness than this.”

Zinser’s review of the National Oceanic and Atmospheric Administration’s fishery enforcement division, which began last year, was prompted by persistent complaints from Northeast fishermen of unfair treatment by officers enforcing fishery regulations governing things such as where and how often fishermen can fish.

A preliminary report released in January found that the abuse allegations weren’t widespread. But it said the process for deciding penalties appeared arbitrary. That report also prompted an audit that revealed widespread mismanagement at the law enforcement office, including the misuse of fines collected from fishermen to buy items such as a luxury undercover boat.

And in April, the office’s former top cop, Dale Jones, was removed after he allegedly ordered dozens of documents destroyed during the investigation.

U.S. Rep Barney Frank, a Massachusetts Democrat, said Locke has restored some of trust in the law enforcement agency, but “they understand they can’t restore trust with words. It’s got to be actions.”

For Thursday’s final report, Zinser looked in detail at 27 complaints about the law enforcement office dating back to 2001, and ruled 19 needed additional review.

Zinser also cited a “troubling pattern” of fishermen settling their cases, rather than going before a judge. He said the agency imposed excessive fines and charges in order to “force respondents into settlement” rather than risk paying a full penalty if they lost before judges they weren’t convinced would be fair.

Zinser noted that between July 2004 and June 2009, fishermen were assessed $5.5 million in fines. But he said they ended up settling for a total of $1.6 million, 70 percent less.

He also singled out a “senior law enforcement attorney” in the Northeast, identified as Charles Juliand by several people, including Rep. Frank, for appearing to show “animus towards members of the regulated community.” He cited various notes Juliand wrote in case files, including instructions to “jack up” the fine on one fisherman and “I think not, sir!” on a letter from a fishermen who wrote he had tried to act in good faith.

In a statement, the National Weather Service Employees Organization, which represents Juliand, called Zinser’s investigation flawed and politically motivated and said some scientific reports indicate fishing fines might actually be too low to deter overfishing.

Juliand said through the group that he had “adhered strictly to the statutes, regulations and agency policies governing the prosecution of marine resource violators. In my 28 years of service, I have never had a single negative review from the NOAA management attorneys for whom I work.”

Since the January report, NOAA has made several reforms, including putting the burden on justifying fines on the agency rather than the fishermen, having the NOAA comptroller oversee the fund that holds fishermen’s fines and communicating better with fishermen on the complex rules.

In a statement, NOAA head Jane Lubchenco said she remained “fully committed to addressing any and all problems identified.”

“Fair and effective enforcement is essential to our ability to rebuild and protect the public’s fisheries and other natural resources,” she said.