A state agency charged with policing Long Island's fisheries failed to process years of vital fishing reports, had inadequate procedures for returning proceeds seized in fishing arrests and improperly allowed arresting officers to negotiate plea bargains, a state probe has found.

The findings follow a three-year probe of the New York Department of Environmental Conservation by state Inspector General Catherine Leahy Scott. Newsday obtained a draft copy of the report, which is scheduled to be released this week after years of delays.

Dozens of Long Island fishermen and women volunteered to be interviewed in the probe, but some of their concerns, including long-term moratoriums and restrictions on transferring fishing permits, aren't directly addressed in the report.

A state official familiar with the investigation explained, "Those are DEC regulatory matters that are outside the purview of the Inspector General's probe."

The investigation followed complaints by commercial fishermen and state lawmakers, and reports in Newsday, that raised questions about the DEC's search and seizure policies. Some fishermen acquitted of charges said the DEC sold their fish, but never returned the proceeds.

While the investigation found that state law "specifically empowers" DEC police to conduct warrantless searches and seizures, it found the DEC "lacked any policies and procedures for the return of property following an acquittal or dismissal of the charges."

As a result of the probe, the agency issued new "evidence control" policies in April 2014, that "places the onus of the return of seized evidence or its value on DEC, not the defendant."

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The probe also addressed the role DEC officers play in negotiating plea agreements with those charged with fishing crimes. According to the report, at least three commercial fishermen alleged DEC officers "pressured them to plead guilty to alleged violations and to negotiate plea agreements and penalties at the courthouse prior to a judicial appearance."

One fisherman alleged an officer threatened to charge him with additional violations "unless he agreed to plead guilty to the original charge and pay a fine," according to the report.

Leahy Scott's report found the practice "may create an appearance of impropriety and coercion," and recommended it be stopped. "An accused defendant should have the opportunity to discuss and negotiate his or her case with an independent prosecutor, not the accusing officer," the report said.

The report says DEC officers now brief prosecutors in advance of court about the case and possible plea recommendations, but aren't directly involved with negotiating with defendants.

In a statement, the DEC said it "cooperated fully with the Inspector General's office and has already made significant changes to its operations."

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DEC said changes include "streamlining permit and licensing processes, hiring more staff to better track licensees not in compliance, and improving internal communications between DEC divisions."

In the course of the probe, inspector general investigators discovered numerous boxes containing years of unlogged daily fishing-trip reports that are required of fishermen to report their fishing haul. Failure to process the reports meant they were not available for databases used for managing the fisheries, and monitoring permit violations.Fishermen must fill out the so-called vessel trip reports each time they take a fishing trip, and logging the reports helps state and federal agencies monitor fisheries, and ensures compliance with quotas and regulations. The DEC receives as many as 15,000 of the reports each year, and reports from 2008 to 2011 were not processed, the state found.

"With the exception of horseshoe crab and striped bass data -- harvest quotas managed by DEC -- no vessel trip report data was inputted into a database jointly utilized by state, regional and federal coastal resource agencies along the Atlantic coast to make marine resource management decisions," the probe found.

The DEC also fell short when it came to marshaling its internal forces to acquire and spend state and federal grants it planned to use to hire an outside contractor to process the trip reports. The report says DEC has since hired staff to enter the reports and caught up with much of the work.

Fishermen can have their permits revoked for failing to file the reports.

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"DEC has ineffectively monitored vessel trip report compliance and violations as they relate to the permit process, and as a result, reissued permits to fishermen who are delinquent in their submission of vessel trip reports or who have received violations," the investigation found.