The deputy director of Massachusetts' marine fisheries has charged that the federal groundfish catch share system has allowed big trawlers designed for offshore fishing to pillage cod from the inshore waters of Stellwagen Bank.

David Pierce, who is also a member of the New England Fishery Management Council, made the allegation during the Wednesday afternoon session of the council meeting in Portsmouth, N.H., where the panel had been struggling to come to grips legally, economically and politically with the findings of a new NOAA Science Center assessment that inshore or Gulf of Maine cod stocks are collapsing.

The intense pressure on the inshore cod population by boats of more than 70 feet has been one of many mutually inclusive theories for how the most important food fish for the region's commercial and recreational industries seems to have gone from robust to threatened in a matter of three years.

The council approved a compromise motion that urged the National Oceanic and Atmospheric Administration to institute cutbacks in inshore cod landings in the range of 10 percent to 23 percent.

NOAA officials promised a quick decision, but also announced a second meeting next Friday in Portsmouth for an industry and NOAA working group on the cod crisis.

The Times, on multiple occasions over the past year, has referred to unattributed claims by small boat owners that offshore trawlers were taking enormous quantities of cod from Stellwagen in single tows while on the way in or out of the ports of Gloucester and New Bedford.

The dire 2011 inshore cod assessment repudiated the previous assessment from 2008, which showed the stock all but fully rebuilt.

Pierce on Wednesday described multiple schemes — made legal or viable in the catch share management system put in place beginning May 2010 — that have put enormous fishing pressure on the cod stocks of Stellwagen and other inshore fishing grounds.

These include the trading or selling of fishermen's catch shares from inshore to offshore boats and across gear types, and the accumulation of quota by the biggest and best capitalized owners.

"We need to address the transfer from small to larger boats," said Pierce, who argued that the system worked to tilt the playing field in favor of the best capitalized and major corporations.

"Sector vessels," members of fishing cooperatives that are allowed to participate in the catch share system, "are in a position to fish in the Gulf of Maine with no catch limits and so they can and do have (harmful) impact," he added.

Pierce's points were corroborated at the meeting by several members of Sector 10, which encompasses day boats in ports south of Gloucester to Cape Cod. They described big boat "pulse fishing" on Stellwagen in response to word that the cod were in.

"What's going on is an indictment of the catch share plan," said Sector 10 President Ed Barrett, who predicted that conservation measures in response to the cod crisis "will ensure that no small boats will be fishing next year."

Catch shares have been held out as a panacea to overfishing by NOAA administrator Jane Lubchenco; the Environmental Defense Fund, where she had been a board director prior to taking the reins of NOAA; the Walton Foundation, organized by Wal-Mart heirs; and other nonprofit foundations funding the transition to catch shares.

A closely related problem is the council's preliminary work gathering input on whether it needs to establish ownership limits on catch shares and other policies designed to encourage fleet diversity between large and smaller fishing businesses.

In Gloucester on Monday night, Pierce and a council colleague heard the leadership of the Gloucester-based Northeast Seafood Coalition and the separate but closely related Gloucester Fishing Community Preservation Fund urge the government to let the catch share system solve problems of fleet diversity and consolidation.

Joe Orlando, who owns and operates the mid-sized trawler Padre Pio out of Gloucester and serves on the coalition board, said any limit to the trading of catch shares between small and large boats would freeze up the market.

"I should be able to buy and sell just like any corporation," said Orlando.

Jackie Odell, executive director of the coalition, which organized 12 of the 17 sectors in the catch share groundfishery, and Vito Giacalone, policy director of the coalition and president of the preservation fund permit bank, said the system created by NOAA for the groundfishery was not a bona fide allocation of the fishery and didn't involve the required referendum. So worrying about consolidation and accumulation caps under the current system makes no sense.

Pierce, however, referred them to National Standard 4 in the Magnuson-Stevens Act which requires all fishery plans to avoid allowing individuals, corporations, or other entities to acquire "an excessive share" of fishing privileges.

At Wednesday's council session, Odell and Giacalone supported a majority of councilors who overwhelmingly rejected Pierce's motions to urge NOAA to add to any interim cod provisions limiting boats to fishing in only one geographic region — either inshore, offshore or Southern New England.

In an emailed Thursday report to coalition members — a report leaked to the Times — Odell also noted that the observed and controversial practice of the big offshore boats starting their trawls outside the Gulf of Maine in Georges Bank — albeit landing fish from inside the Gulf and then reporting them to be Georges Bank fish — was legal.

"The law indicates that the fish caught be reported in the stock area where the fish is hauled up," she wrote to members. "If the council sees this as being a problem, then the regulation which directs this reporting should be revised."

In his presentation to the council, however, Pierce called the practice "misreporting."

"(It's a) misreporting of Gulf of Maine and Georges Bank cod," he said.

Richard Gaines can be reached at 978-283-7000 x3464, or rgaines@gloucestertimes.com.

The federal government, and the fishing industry — the commercial and recreational sides alike, with deep dependence on inshore or Gulf of Maine cod — have entered uncharted waters found by NOAA to hold far fewer cod than anyone could have guessed just months ago.

Now, what to do about the cod crisis sits at the top of the agenda of the New England Regional Fishery Management Council this Wednesday afternoon in the middle of its three-day February meeting in Portsmouth, N.H.

Signaling the depth of the dilemma and joining the deliberations will be Sam D. Rauch III, the nation's acting assistant administrator for fisheries, "along with many of my key staff," Rauch announced at the end of a lengthy letter sent late last week to the council.

It was dated Thursday, the day after the dire results of a 2011 stock assessment was vetted by the council's independent Science and Statistical Committee meeting in Providence, R.I.

Despite much uncertainty about the correctness of the new assessment — it undercuts its 3-year-old predecessor assessment — Rauch outlined the limited legal options available, given the finding that the inshore cod stocks had been overfished and remain subject to overfishing.

A routine response to these findings could be a complete shutdown of the fishery, but even allowing 500 metric tons to be harvested would cost the ports of Gloucester and New Bedford as much as $170 million, according to economic modeling by the National Oceanic and Atmospheric Administration and data presented to the Science and Statistical Committee last week.

Rauch wrote that federa; Secretary of Commerce John Bryson was prepared to receive a request from the council to implement "an emergency or interim action" on cod that would "reduce" rather than "end overfishing." But he also emphasized that any "emergency/interim" plan would be required by law to "make a substantial reduction in overfishing and must, at a minimum, not further deteriorate the condition of the stock."

Until word leaked out about the 2011 assessment late last year (covering the period 2007 to 2010), the government, the industry and even hard-line environmental groups had been operating on what has become officially labeled as false and befuddling information — that of all the troubled stocks in the New England multi-species mix, Gulf of Maine cod was on the most desirable trajectory of all, rebuilding toward sustainability.

Rauch made this point abundantly clear in his letter.

"The lack of adequate progress was not due to any failure on the part of the New England Fishery Management Council to take necessary action to meet the requirements of the Magnuson-Stevens Act," he wrote.

"Nor was it due to any failure on the part of fishery participants to act in compliance with applicable regulatory measures," he wrote. "Rather, the lack of adequate progress is due to a new and significantly revised understanding of the condition of the stock since the 2008 assessment was completed."

His letter also emphasized the uncharted nature of the cod problem entailed in meeting the conservation mandates in the Magnuson-Stevens Act while remaining true to the same law's charge to protect the economies dependent on the fisheries.

"As the National Marine Fisheries Service and its regional management council consider pursuing this unprecedented approach to addressing the unique situation we are now in with Gulf of Maine cod," Rauch wrote, "we recognize there are many policy determinations that must be addressed for the first time and that the council will require guidance from the agency.

In early January, NOAA Administrator Jane Lubchenco rejected U.S. Sen. John Kerry and Gov. Deval Patrick's requests for a new assessment before deciding how to manage inshore cod in the fishing year that begins May 1.

Richard Gaines can be reached at 978-283-7000 x3464, or at rgaines@gloucestertimes.com.

New England's fishery management council committee holds an all-day meeting Wednesday in Providence to examine and debate a new, dire and skeptically received assessment of the Gulf of Maine cod stock.

Directly contradicting an assessment in 2008 — which found the most important wild resource of the New England groundfishery was recovering rapidly from chronic overfishing — the 2011 assessment concluded that the cod stock is so weak that nearly all fishing for it should be halted.

But the assessment, a product of the NOAA Science Center in Woods Hole, has been received with doubts about its accuracy, and the National Oceanic and Atmospheric Administration's science itself has come under intense criticism.

In the furor, U.S. Sen. John Kerry, Gov. Deval Patrick and the co-chairmen of the Massachusetts Marine Fisheries Institute have written to NOAA Administrator Jane Lubchenco and top Obama administration fisheries officials, advising them that a "new cod assessment, undertaken with industry and 'local scientific experts'" was essential to gain the "trust and support of fishermen."

But Lubchenco wrote back to Kerry on Jan. 9 that time constraints made it impossible to organize a new stock assessment in time to set catch limits for the 2012 fishing season that starts May 1.

"So we have to use science that we're all questioning to make drastic measures?" Laura Ramsden of New Bedford, an owner of the M. F. Foley Fish Co. and a member of the council asked at a subcommittee session last week.

How peer-reviewed stock assessments three years apart could be so far off has left scientists and fishermen shaking their heads and brought uncertainty to immediate and midrange cod catch limits and management policy.

The 2011 assessment estimated the spawning stock biomass in 2007 at 10,778 metric and total biomass at 17,757 metric tons. Both estimates are about one-third the size of the stock estimates in the 2008 Gulf of Maine stock assessment, which has been the foundation of catch limits that have not been violated.

"There is no reason to believe that the current information is any more reliable than the 2008 assessment. Both cannot be correct," said fisheries scientist Steve Cadrin, a member of the regional management council's Science and Statistical Committee, which hosts Wednesday's assessment meeting at the Hotel Providence, and a member of the faculty at University of Massachusetts Dartmouth.

Cadrin, a former chairman of the Science and Statistical Committee, said he found many problems with the 2011 assessment that raises doubts in his mind that it was closer to right than the 2008 assessment.

"There are major uncertainties in the geographic stock definition, fishery monitoring data, survey calibrations, modeling assumptions, overfishing definitions and rebuilding targets," Cadrin said. "Some important sources of uncertainty are greater now than they were in 2008.

"For example," he continued, "there was no change in survey vessels that affected the 2008 assessment, and the estimate of recreational catch was more realistic in the 2008 assessment."

The trawl surveys done in advance of the 2008 assessment were all conducted by the NOAA research vessel Albatross IV, but the surveys done for the 2011 assessment were by Albatross and its successor, the Henry B. Bigelow.

Dimensionally, the boats differ, and industry experts who advised NOAA on the design of the trawl package for the Bigelow have been quoted as saying the boat and its trawl dimensions were mismatched.

Russell Brown of the NOAA Science Center discounted the concerns expressed by net designer Tor Bendiksen of Reidar's Manufacturing in Fairhaven and gear designer Bob Taber, of Trawlworks Inc. in Narragansett, R.I.

Cadrin also identified what he described as "weird" recreational catch reports, which figured into the pessimistic findings of the 2011 stock assessment.

"The estimate of catch from the recreational fishery in 2010 is unusually high for a few reasons," Cadrin said in a series of emails to the Times in response to a query.

"The recreational catch in 2010 is estimated to be greater than the commercial catch," he said. "About half of the recreational catch (a quarter of the total catch) is estimated to have come from two weeks in the spring of 2010. More than half of the recreational catch in 2010 is estimated to have come from private boats — not charter or party boats.

"These estimates are difficult to believe," Cardin added.

Brian Rothschild, Cadrin's colleague at UMass-Dartmouth's School of Marine Science and Technology, had a subtly different take on the clashing cod stock assessments. He said he was not ready to decide between the assessments, but he said it is the burden of the Science Center to explain how its work could be so contradictory.

Gene Martin, NOAA's chief regional counsel, offered preliminary advice to the regional council's Groundfish Committee meeting in Portland last week.

He that a very close reading of the Magnuson-Stevens Act gives the government some limited flexibility under emergency circumstances to allow overfishing to continue but only for "one year."

"At best, this is a short-term delay," Martin said.

Richard Gaines can be reached at 978-283-7000 x3464, or rgaines@gloucestertimes.com.