The outlook for the fisheries is improving, a leading federal administrator told a congressional panel in Boston early this week, but lawmakers were unconvinced.

Instead, at a packed hearing at the statehouse on Monday, legislators hammered NOAA administrator Jane Lubchenco for her department’s administration of the region’s new catch shares fisheries management system. It has been a year since the new quota-based system has been in place and Ms. Lubchenco, the ex-officio head of the National Marine Fisheries Service (NMFS), touted the progress of the region’s long-suffering fisheries to an unsympathetic congressional panel.

“We are finally on track to end overfishing,” she told the panel of congressmen that included Massachusetts Sens. John Kerry, Scott Brown and Alaska Sen. Mark Begich as well as Massachusetts Reps. William Keating, Barney Frank and John Tierney.

“Stocks are being rebuilt and catch limits are up,” Ms. Lubchenco said. “In addition revenues are up for some but not all the fishermen. Fishermen are fishing more selectively, benefiting their bottom line and the vulnerable stocks. I believe that in fact we are making progress but not enough.”

The new management plan was instituted a year ago, after years of planning, to end the so-called “race for fish” that contributed to the devastating groundfish collapses of the past two decades when fishermen were allocated days at sea rather than a quota of fish to catch. Under the catch share system, fishermen in 19 different sectors throughout New England are able to buy and lease catch allocations on a free market basis, one that Senator Kerry argued puts small boat fishermen and coastal communities at a disadvantage. As he noted, in the past year 80 per cent of landings had been brought in by 20 per cent of vessels in the region.

“If catch shares result in so much of the landings going to so few of the fleet, something is wrong,” Mr. Kerry said.

But Ms. Lubchenco said the trend predated the new sector-based program.

“If you look at changes from the year 2001 to 2009, landings dropped by 40 per cent, revenues fell by over one half and the number of vessels dwindled to half their previous levels,” she said. “What we’re seeing in the last year is not surprisingly a continuation of some of those changes.”

Mr. Kerry also pressed Ms. Lubchenco to support a disaster declaration for the region’s fishing industry.

“When the government steps in and creates a dislocation rather than Mother Nature and people are selling their boats and their homes we have a disaster, an economic disaster,” he said.

Ms. Lubchenco said she would back providing support to fishermen when circumstances warranted and said her administration was waiting for a request from Gov. Deval Patrick for assistance to the hardest-hit regions.

“The fact that the economic situation is so serious and has been on the decline for so long puts us in a very, very challenging position,” she said. “It’s hard for people to trust a process where the economics stink for many of them. I totally understand that, that’s why I am committed to turning things around and I believe that finally we are on the path to do that . . . We have seen increases in catch limits in 12 of the 20 groundfish stocks this year because the rebuilding has begun. We’re turning the corner but we have a long, long way to go.”

While acknowledging that the program had caused hardship on some fishermen, Ms. Lubchenco said from an environmental perspective the program was working. Catch shares requires a new level of accountability in documenting fish brought on board and Ms. Lubchenco illustrated how the augmented monitoring effort had paid off. In 2010 nine per cent of the total Georges Bank yellowtail flounder catch was discarded, compared to 31 per cent in 2009. But stepped-up monitoring also comes with a cost. Boats are sometimes required to bring at-sea observers on board during fishing trips; the government paid the tab for this last year, but with large federal budget cuts looming, many fishermen expect that will end.

Stephen Welch, who operates a 55-foot gill net and a 45-foot trawler out of Scituate, told the panel that it may become unprofitable for him to go fishing.

“It’s cheaper for me to stay at home and lay off six employees between two boats than to actually go fishing under catch shares and that’s what I did last year,” he said. “I felt like I wasn’t doing my responsibility as an American citizen to sit at home and lease out my quota. It’s an injustice to the American people. If we have to pay for monitoring next year out of our own pockets, then I’m quitting fishing and I will stay home and become a welfare armchair captain.”

Ms. Lubchenco said pilot programs to test the effectiveness of cheaper electronic monitoring systems are in the works. Mr. Kerry was skeptical.

“I would like to remind everyone that this comes into the discretionary portion of the federal budget which took $1 trillion worth of cuts in the course of the last few weeks,” he said.

Sen. Scott Brown, who is up for reelection next year, was unsparing in his critique of Ms Lubchenco’s administration. Citing dreary statistics about groundfish collapses from a period before the catch-share system was enacted, he called the NMFS relationship with fishermen “beyond repair.”

“Since I’ve been working on this issue I’ve seen a complete lack of trust between every type of individual business and the federal government,” he said.

Countering charges that her administration was out of touch with the fishing community, Ms. Lubchenco said in the past year and a half she had spent 40 hours meeting with fishing groups and only three hours with environmental groups.

Cong. Barney Frank was more colorful in his criticism, calling Ms. Lubchenco’s testimony “self-congratulatory” and “resentful” of the fishing community. Mr. Frank represents the 4th Congressional district, an area that includes New Bedford.

“Most federal agencies are advocates of the people in their names: the Veterans Administration, the Small Business Administration, the Department of Agriculture,” he said. “There are only two regulatory agencies that I can think of that have a genuinely hostile attitude toward the people under their control: the National Marine Fisheries Service and the Drug Enforcement Agency.”

Mr. Frank pointed out that although the price per pound for fish landed in New England had increased in the past year, it had not offset revenue losses for the region’s fishing industry totalling $2 million during the same period. Mr. Frank pushed for higher catch limits and criticized the NMFS policy of using the most conservative estimates of fish stocks to set quotas

“Look, I’m proud of my environmental record,” he said. “We’re not talking about permanently fouling anything . . . I don’t know a single fisherman who wants to be the last one to fish.”

Alaska Sen. Mark Begich was alone in his praise of catch shares and offered an optimistic view of the new management program, based on his own state’s experience. Alaska has allocated quotas for the once-overfished halibut since 1995.

“We have had success around these quotas, around catch shares, hard numbers too,” he said. “We’ve had great success in the fisheries that had been devastated by overfishing. They used to fish two days for 24 hours, now they fish for 10 and a half months, we get premium dollar and it’s sold around the world.”