Federal prosecutors on Wednesday charged a Long Island fisherman with wire fraud and falsification of federal records in connection with a scheme they say resulted in the illegal harvesting of more than 86,000 pounds of fluke over three years.

During an appearance at U.S. District Court in Central Islip on Wednesday, Charles Wertz Jr. of East Meadow entered a plea of not guilty to the charges, which stem from fishing that federal prosecutors say took place between 2009 and 2011.

Christopher Hale, a trial attorney for the U.S. Department of Justice's Environmental Crimes Section, said prosecutors were negotiating a plea agreement with Wertz and requested an adjournment until later this month. U.S. District Judge Joseph F. Bianco granted the adjournment.

Wertz, 53, was released on his own recognizance. He and his attorney, Ronald Russo of Manhattan, declined to comment.

Feds charged in a 10-page criminal information that Wertz unlawfully harvested fluke valued at more than $199,000 by manipulating a federal program known as research set-asides. The program allows fishermen to buy additional quotas beyond legal limits. Regulators use the proceeds from set-aside auctions to fund fisheries research.

Feds charged that Wertz and his C&C Ocean Fishery Ltd. in Freeport underreported the actual amount of fluke taken during that three-year period by 86,080 pounds, filing 137 falsified fishing reports via the Internet. The document alleges Wertz took advantage of the research set-aside program by harvesting fluke beyond state limits but failing to properly report the catch against his research set-aside allotment.

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Wertz is the son of Charles Wertz Sr., a longtime commercial fisherman from Freeport who was a vocal critic of federal fishing regulation. The elder Wertz, who pushed hard to change rules that give New York fishing vessels a smaller percentage of the fluke allotment than boats from states such as North Carolina, died in February.

Advocates for New York fishermen say while the younger Wertz's alleged actions, if true, can't be condoned, they also criticized the federal fishing quotas.

New York, with one of the largest fishing fleets on the East Coast, gets 7.6 percent of the federal quota, compared with North Carolina, which gets 27 percent, and Virginia, 21 percent.

Daniel Rodgers, a Riverhead attorney who has represented fishermen and women, said unfair management of fisheries will ultimately drive fishermen from the waters.

"Everyone agrees we need rules, and everyone wants to play by the same rules," he said. "The problem is, we are regulating an industry into extinction. Regulation is not just about saving fish stocks, but also being able to effectively manage an industry. That's where fed regulators have fallen down. Once these fishermen are gone, they are not coming back."

A Department of Justice spokesman declined to comment on regulatory matters.