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The International Pacific Halibut Commission announced Friday that Southeast Alaska's commercial halibut catch limits would drop for the second year in a row.

"The whole thing hurts," said Kathy Hansen, president of the Southeast Alaska Fishermen's Alliance.

The new limit is 6.21 million pounds, a 28 percent reduction from last year and 40 percent from 2006. Eastern Alaska has overfished in the last decade, according to the commission.

In 2006, Southeast had 993 permit holders. They took 19 percent of Alaska's 52.2 million-pound halibut harvest. The value in 2006 of individual fishing quotas held by Southeast residents was estimated at $146 million.

Methods for calculating the catch limit changed this year. For two decades, the total weight of harvested halibut has been estimated separately for each management area. This year the commission used a new system designed to acknowledge that because halibut travel between areas, fishing in one area can affect others.

That's why it was particularly frustrating to some Southeast Alaska fishermen that British Columbia's limit will exceed staff recommendations. In December, staff recommended 8.06 million pounds, but the commission approved 9 million pounds for the area.

"To do anything different from the staff recommendations is to move away from biology and science, and just go for a resource grab," Hansen said.

The commission comprises three Canadians and three Americans. After industry groups present their data to the commission, the final negotiations on harvest levels are secret.

Southeast limits came with a footnote presuming that charter boats would adhere to the yearly guideline given to them, which they have not done in past years. That cap is a guideline, not a firm limit.

"There was some frustration from the commercial sector that the charter sector was trying to maintain the same catch levels as they've had in the past, even in the face of a declining resource," Hansen said.

Charter boat operators could face a cut in bag limits to one fish per person daily. Last year a decades-old two-fish bag limit was modified with a requirement that the second fish be less than 32 inches long.

"This will cut the charter take 58 percent," said Rick Bierman, lodge owner and spokesman for the Juneau Charter Boat Operators' Association. "It's a pretty horrid thing from the perspective of a lodge."

Bierman said he thought Southeast lodges might close as the Kenai Peninsula and other fishing areas with higher limits would become more attractive than Southeast lodges to sport fishermen.

Juneau charter boat captain Chris Condor vowed to fight the limits.

"It's not done yet by a long shot," he said.

The U.S. Secretary of Commerce will take public comments and publish regulations before the commercial season opens in March.

• Contact Kate Golden at 523-2276 or kate.golden@juneauempire.com.