BOSTON – The nation’s top fisheries cop was replaced Thursday after a federal review detailed mismanagement at his agency and showed that he ordered dozens of files destroyed during the investigation.

Dale Jones was removed as director of the National Oceanic and Atmospheric Administration’s law enforcement office and was replaced on an interim basis by Alan Risenhoover, head of NOAA’s Sustainable Fisheries Office.

In announcing the changes, NOAA Fisheries head Eric Schwabb said in an e-mail to employees, “Ensuring a fair and effective enforcement program is our focus moving forward.”

It was unclear whether Jones was fired, put on leave or subjected to some other administrative action. A NOAA spokesman, citing privacy laws, said he could not comment on specific personnel moves.

U.S. Sen. John Kerry, D-Mass., said the decision was “painful at NOAA, but it had to happen.”

“Replacing this official was an important step to clear the air and turn the page,” Kerry said.

Richard Burgess, a fisherman in Gloucester who has fought $85,000 in fines, said Jones’ removal was a first step but the problems go beyond Jones in a corrupt agency that has persecuted fishermen.

“It’s a chip off the iceberg, but the iceberg is full of very bad people,” he said. “Dale Jones is certainly a start, but they can’t stop now.”

NOAA’s law enforcement office enforces the nation’s complicated fishing regulations, which include rules about where fishermen can fish, how much they can catch and the gear they can use. Violators are subject to penalties ranging from $5,000 to $80,000 for a first offense.

Fisherman in the Northeast have complained for years of excessive fines, uneven enforcement and retaliation by fisheries officers.

Last year, NOAA chief Jane Lubchenco requested a review of the office by the U.S. Department of Commerce’s inspector general, Todd Zinser.

His report in January showed that fishermen in the Northeast were given double the fines of fishermen in other regions, and that the process for penalizing violators appeared arbitrary and unfair, but it didn’t uncover widespread abuse.

The report questioned why an agency that deals mainly with civil fines was dominated by criminal investigators. Fishermen said that showed the agency viewed them as criminals.

Zinser also ordered an audit of how fines collected from fishermen were spent when NOAA couldn’t determine how the money was used. Fishermen compared the fines to a bounty, but Jones has said all the money was spent according to NOAA rules.

Last month, Zinser testified before a congressional committee that Jones had ordered up to 140 files destroyed after IG staffers met with him to explain the scope of their review. Zinser said that Jones told him the shredding was unrelated to the review and had been planned long before he learned about it.

The revelation prompted numerous calls for Jones to be fired or to step down.