The U.S. Commerce Department declared a national fishery disaster Thursday in New England, opening the door for tens of millions of dollars in relief funds for struggling fishermen and their ports.

Acting Commerce Secretary Rebecca Blank said the declaration comes amid “unexpectedly slow rebuilding of stocks,” which is forcing huge fishing cuts that are jeopardizing the New England industry. And she said her agency had determined the trouble with fish stocks comes despite fishermen following rules designed to prevent overfishing.

“The future challenges facing the men and women in this industry and the shore-based businesses that support them are daunting, and we want to do everything we can to help them through these difficult times,” Blank said.

The declaration doesn’t guarantee any money will actually be funneled toward fishermen, but U.S. Sen. John Kerry said it’s a big step forward.

Senate Majority Leader Harry Reid has committed to include $100 million for fishermen and fishing communities in emergency assistance legislation that will be debated during the lame-duck session after the election, Kerry said Thursday.

Lawmakers must now fight for the money in a potentially reluctant Congress, he said.

Kerry compared fishermen to farmers, saying they’re just as dependent on the vagaries of the ecosystem as farmers are, and just as deserving of assistance when things go bad through no fault of their own, like when farmers face a drought.

“We put billions into the heartland of our country for farmers, billions, literally,” said Kerry, a Massachusetts Democrat. “When you have a massive layoff of an industry like that because of circumstances that are entirely outside the fishing industry’s control, we have to respond as a country.”

Federal and state lawmakers have pursued the disaster declaration since 2010, when new regulations were enacted in New England that put tough limits on how much fishermen can catch of a given species.

In the two years since, federal scientists have reported key stocks aren’t rebuilding quickly enough, including cod in the Gulf of Maine and yellowtail flounder in the Georges Bank fishing grounds off southeastern New England.

Cuts in the allowed catch have already been enacted, but ruinous catch reductions are projected for the 2013 fishing year that have put the future of the historic industry in doubt.

The money in the $100 million aid package forwarded by Kerry includes direct aid to fishermen and money to cover required costs, such as the independent observers to monitor their catch. It also includes funds to improve fishery science and stock assessments, which fishermen complain are inaccurate.

The Northeast Seafood Coalition, an industry group, applauded the disaster declaration and said regulations are needed that better account for how fisheries fit into the larger environment.

“It is unfair to hold fishermen exclusively accountable for natural cycles of complex ecosystems,” the coalition said.

Johanna Thomas of the Environmental Defense Fund said a better grasp is critically needed on how fish abundance is affected by factors such as climate change, pressure on local coasts and warming ocean temperatures.

“The problems facing the fishery … are long-term and the solutions should be also,” she said.