BOSTON — The U.S. commerce secretary has reversed course and will allow more fishermen who have been accused of violations to have their cases reviewed for fairness by a special investigator.

Gary Locke also has agreed to give the investigator discretion to freeze pending penalties against fishermen, according to Sen. John Kerry’s office, which released the information after The Associated Press reported on the changes ahead of the official announcement this afternoon.

Locke had denied both requests in January, prompting protests from regional lawmakers who said it was another assault by the federal government on the Northeast’s fishing industry.

Locke and Jane Lubchenco, head of the National Oceanic and Atmospheric Administration, met earlier this month with Kerry. Last week, Kerry wrote a letter requesting, among other things, the concessions that Locke is granting.

Kerry called Locke’s move a “welcome first step to repair the relationship” between fishermen and government regulators.

“Our fishermen, fishing communities and the Massachusetts congressional delegation have been ringing this alarm bell and this is very welcome news that the government is responding,” Kerry said in a news release.

Richard Burgess, a Gloucester fishermen who has fought $85,000 worth of fines for what he describes as minor bureaucratic and paperwork violations, said Locke’s move is a start but that more needs to done to make things right.

“We’ve just been lied to, and we’ve been cheated and it’s about time somebody did something,” he said.

The nation’s fishery laws regulate, among other things, the types of gear fishermen can use, when and where they can fish and how much of a given species they can catch.

In 2009, Lubchenco ordered a review of the law enforcement system, following years of complaints by Northeast fishermen of bias, retaliation and excessive fines.

Last year, the Commerce Department’s inspector general released a report that gave examples of abusive treatment of fishermen, though it said such treatment was not widespread. The report said the region’s fishermen were given double the fines of other regions and the process for penalizing violators appeared arbitrary and unfair.

The former head of the law enforcement agency, Dale Jones, was removed after it was learned he had ordered dozens of documents shredded during the investigation.

Fishery enforcement officials have said the inspector general’s investigation was flawed and politically motivated. They also say it scapegoated law enforcement officials who have been professional and fair in their work to protect the fishery.

The inspector general also highlighted several possibly questionable penalties against fishermen, and Locke appointed retired judge Charles Swartwood as a “special master” to review the cases.

Fishermen and lawmakers then asked for more time to file additional complaints for Swartwood to consider, saying the fishermen had been hesitant to do so in a system they considered biased.

Locke initially said the inspector general’s office had worked hard to ferret out cases with possible abuse and expressed doubt that large numbers of fishermen were still waiting to be heard. He said “the importance of finality” required placing some limits on the number of cases to be reviewed.

He also said if he allowed penalties to be suspended, it could be seen as prejudging the outcome of Swartwood’s review.

Now, Locke has agreed to open a 51-day window to allow fishermen and businesses to file new complaints. Swartwood will be able to grant a stay of penalties against fishermen, if he chooses.

NOAA also has agreed to an independent audit of the fund that takes in the fines fishermen pay for violating fishery law.

The agency had been criticized for poorly tracking the fund, and for using the money on expenditures such as vehicles for fishery enforcement officials and a luxury undercover boat. It has changed policy to forbid those funds from being used on vehicles or boats, according to the people familiar with the decision.

NOAA is also announcing a new policy on penalties that ensures Massachusetts fishermen aren’t subject to higher fines than people from other regions.

Earlier this month, President Obama nominated Locke as the next U.S. ambassador to China. Kerry is the chairman of the Senate Foreign Relations Committee, which reviews such nominations.