BOSTON – New England’s fishing industry changes dramatically today under new rules that promise autonomy for fishermen and better protection for fish but have so far inspired uncertainty.

“To me, it gives us more opportunity,” said Peter Taylor, a fisherman from Chatham, Mass.

Meanwhile, in Gloucester, fisherman Joe Orlando said, “I guarantee you in three months’ time, there’s going to be total chaos.”

The new regulations replace a system that was broadly unpopular and tried to stop overfishing by making fishermen less efficient, with steps such as slashing the number of days they were allowed to fish.

Hundreds of boats went out of business over the last several years as some fishermen were reduced to as few as 24 fishing days a year. But 12 of the 19 federally managed stocks of groundfish are still considered overfished.

Regulators hope for better results in the new system, which sets strict annual catch limits on groundfish species, such as cod and flounder, then divides the catches to be managed by groups of fishermen, called sectors.

The idea is to give fishermen a chance to use their skills to avoid certain protected species and haul in more abundant fish when the market is right. It also eliminates the hated practice of throwing away fish, which fisherman had to do under the old system when they exceeded their daily limits for certain species.

About 800 boats out of the region’s roughly 1,500 are in sectors, and those boats have recently accounted for about 98 percent of the fish caught in the area.

The sector system is optional but has been chosen by nearly all fishermen, who view staying with the old system as even more restrictive. Environmentalists love the change, saying it establishes tough and overdue protections for fish.

But fishermen say regulators set catch limits so low on species such as pollock that their allotment will be quickly reached and sectors will be forced to shut down prematurely.

Lawmakers in the Northeast have asked Commerce Secretary Gary Locke to increase the catch limits, and will meet with him May 12.

Orlando, the Gloucester fisherman, said the low allocations come from a radical undercounting of fish stocks by scientists.

“If the government wants this to really work, they’ve got to throw some more fish into the system,” Orlando said.

A new survey of fishermen indicates that most view the change with skepticism.

The survey, funded by the Environmental Defense Fund, which supports catch-shares, included 172 interviews, including several with fishermen who won’t be affected by the switch. It shows that 46 percent of respondents oppose sectors, with another 37 percent offering only qualified support. About 18 percent support the switch.

The study also showed confusion among fisherman, which co-author Richard Pollnac, chairman of the University of Rhode Island’s marine affairs department, said could indicate that regulators moved too quickly to overhaul the system in one year.

Fisherman Brian Loftes of Point Judith, R.I., opted to stay in the old system. He believes the change is doomed to fail because of paltry catch allotments and the incompetence of federal management. He points to years of sacrifice that have only led to more cuts and flawed regulations that prevent fishermen from catching the fish that have rebounded.

During the last fishing year, for instance, fishermen caught just 25 percent of their 24.5 million-pound allocation of haddock, federal statistics show.

Patricia Kurkul, Northeast regional administrator for the National Marine Fisheries Service, said poor management isn’t to blame for ever-tighter regulations — overfishing is.

There haven’t been enough fish to support the number of fishing boats, and the fleet needs to shrink further, she said. The flexibility in the new system aims to make the cuts easier to bear until stocks get healthier.

Federal regulators project a loss in revenue for groundfishermen, from $85 million in 2008 to $63 million in 2010, but say that loss could be reduced if fishermen learn to better tap into the healthy stocks such as haddock.

Kurkul added that regulators have learned from two small sectors that have operated off Cape Cod for several years.

Taylor, who’s in one of those sectors, said the change is causing angst, but offers hope for boats that learn to fish more efficiently, avoiding vulnerable species while snagging more abundant fish.

“That’s the key, to put together a clean fishing operation,” Taylor said. “And if you can, you can stay fishing.”