An East Northport commercial fisherman who was once an outspoken critic of federal regulators was indicted Tuesday on charges of conspiracy, mail fraud and falsification of federal records in connection with the illegal harvest of more than $400,000 worth of fluke, authorities said.

A federal grand jury returned the indictment against Thomas Kokell, a North Shore clammer who once operated a commercial trawler at Point Lookout. Kokell in 2007 was hit with a $120,000 fine for separate overfishing charges, a fine that was later reduced after intercession by Sen. Chuck Schumer (D-N.Y.).

Kokell is the latest Long Island fisherman to be indicted in a wide-ranging federal probe of a program that allows boats to harvest beyond seasonal limits and quotas. To date, more than a half-dozen men have pleaded guilty to charges and sentenced to large fines, loss of fishing licenses and prison.

Prosecutors with the U.S. Department of Justice’s Environmental Crimes section charged Kokell was involved in a scheme to cover up the illegal harvest of 196,000 pounds of fluke by falsifying dozens of fishing trip and dealer reports, which are required as part of commercial fishing regulations.

The case against Kokell was investigated by agents of the National Marine Fisheries Service.

Authorities said Kokell will be arraigned in Central Islip at an unspecified future date.

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Peter Smith, a Northport-based lawyer for Kokell, said his client will plead not guilty. Smith said he planned to conduct an investigation into the charges, but expressed concern that the new charges may be related to his client’s criticisms of federal enforcement actions in a series of Newsday stories beginning in 2010. Kokell didn’t return calls seeking comment.

Kokell is the latest to be charged as part of a federal probe of a program called research set-aside, which allows fishermen to pay for the right to catch fish beyond set quotas and seasons.

Prosecutors have dubbed the program a “license to steal” because some fishermen who paid to be in the program by bidding on large blocks of fishing quota didn’t properly report all the fish they had caught. Proceeds from the set-aside auction helps fund fishing research programs. The program has been suspended as charges have been filed.

Kokell had been an outspoken critic of federal and local enforcement actions and excessive fines against fishermen, and he won the high-profile support of officials such as Schumer.

Kokell in 2011 had a balance of $30,000 in fines for overfishing forgiven at Schumer’s urging after an inspector general for the National Oceanic and Atmospheric Administration found that forfeiture funds, obtained through fines levied against fishermen and through selling seized property, were improperly used to purchase vehicles, boats and international travel for employees of the Northeast region of the National Marine Fisheries Service. The report found that fines levied against fishermen in the Northeast region were more than two times higher than those in other regions throughout the country.