Responding to the complaints of fishing communities throughout the Commonwealth on Tuesday, the Patrick administration agreed to implement a $1 million loan program to help small fishermen get back on the water.

“Massachusetts has a proud tradition of commercial fishing, and these direct loans will help preserve the economic viability of our fishing ports and communities,” Gov. Deval Patrick said on Tuesday.

For the past year, as the National Oceanic and Atmospheric Administration has put its new catch shares program in place, many small fishermen have seen themselves shut out of the catch allocation sweepstakes. The catch shares program awards fishermen a yearly allocation of poundage of fish. It replaces the old days-at-sea program, which allocated time on the water. Scientists had argued that program was responsible for the so-called “race for fish” that pushed many groundfish species to the brink in recent decades.

In October, NOAA chief Jane Lubchenco told Massachusetts lawmakers that since the catch-shares program was enacted, many of the region’s groundfish stocks, like the yellowtail flounder, had already shown signs of improvement. But the news came as little relief to the region’s fleet of owner-operated fishermen, many of whom found themselves priced out their livelihood.

At the heart of the problem are the quota allocations themselves, which small fishermen like the Vineyard’s Greg Mayhew have said are skewed towards large, politically-connected factory fleets. Catch allocation is based on a vessel’s catch history from 1996 to 2006, a period of relative scarcity when small fishermen say only the most irresponsible ships were still trawling on hallowed fishing grounds like Georges Bank. Fishermen shut out of those allocations are able to purchase more quota on the open market but are often at a disadvantage to larger fleets, which benefit from economies of scale.

As a result, the past year has seen increased consolidation among the state’s fishing fleet as 80 per cent of its landings were brought in by 20 per cent of its vessels, and smaller operators struggled to the bear the increased monitoring costs essential to the new program. The Vineyard, once storied for its fishing fleet, now counts Mr. Mayhew and his son Todd as the only active groundfishermen left on the Island with federal permits.

The new loan program announced on Tuesday is intended to reverse that trend. The loans will specifically help small fishermen purchase back some of that catch allocation and help “ease the transition” to catch shares, according to Mr. Patrick. This week lawmakers who had criticized the Patrick administration and NOAA in the fall indicated their approval.

“Every dollar of economic assistance matters to fishermen who have been hanging on by their fingernails,” said Sen. John Kerry. “This revolving loan fund is a no-brainer. Access to capital has been very difficult and this fund is another tool in our toolbox to help keep small boat fishermen in business.”

Sen. Scott Brown, who has been perhaps the most outspoken critic of the program, grudgingly applauded the move.

“I’m glad there will be additional support for Massachusetts fishermen struggling to survive under catch-share management,” he said. “I am committed to holding NOAA accountable for their regulations and ensuring that our fishermen have a fair management system based on sound science.”

But that science faced renewed questions this week after federal regulators reaffirmed a dreadful assessment of cod in the Gulf of Maine that would see a mandated reduction of 90 per cent catch on those fishing grounds. But on Thursday federal regulators relaxed those mandated cuts for the next year in the face of criticism from the fishing community, which argued that the move would put even more fishermen out of business and was at odds with what they were seeing at sea.

In the meantime, the state is seeking loan-administration partners for its new program and invites eligible fishermen to visit for updates and to learn where they can apply for the loans.