The fight over what’s best for Maine’s groundfish didn’t end with the new Amendment 13 rules that took effect earlier this month.

Wednesday, two of the environmental groups responsible for the original lawsuit that led to the new rules governing the catch of a dozen species of fish including cod, haddock and flounder, filed a complaint in federal court stating that Amendment 13 did not satisfy their concerns and asking a federal judge to take action.

The Conservation Law Foundation and Natural Resources Defense Council’s complaint states that Amendment 13 violates federal fisheries law because it does not provide adequate protection for five struggling populations: Georges Bank cod, American plaice, white hake and two populations of yellowtail flounder, those in the southern New England, mid-Atlantic region, and those in the Cape Cod, Gulf of Maine region.

“We view it as a crisis situation, for Georges Bank cod in particular,” Roger Fleming, a Rockland-based attorney for the Conservation Law Foundation said Wednesday. “We think it’s absolutely necessary.”

While parts of Amendment 13 are good policy, other portions either fail to accomplish or completely ignore goals of reducing overfishing and rebuilding struggling fish populations, Fleming said. For example, statistics indicate that fishing for cod has exceeded what would be sustainable in the long term since the 1970s, often by more than double, according to CLF and NRDC. Unless overfishing is stopped, the population could crash and never recover, Fleming said.

Fleming and his fellow environmentalists have made many of these arguments questioning the efficacy of Amendment 13, since the rules came out in draft form earlier this spring. Like the old rules that prompted the original 2001 lawsuit, these regulations just don’t end overfishing, he said.

However, industry and government officials throughout New England complain that the Amendment 13 rules, which cut fishermen’s access to the resource significantly, is already too strict, reducing some boats’ fishing days by as much as 30 percent. Maine’s Department of Marine Resources favors a slower timeline for rebuilding fish populations to ensure the economic stability of fishing communities.

“It will make it that much harder for [Maine boats] to continue fishing,” Department of Marine Resources Commissioner George LaPointe said of CLF and NRCM’s action.

But the state wasn’t surprised by Wednesday’s announcement, and DMR intends to study the allegations and participate in whatever legal actions ultimately result, LaPointe said.

The environmental groups have not asked that any changes be made before next year’s fishing season opens in May 2005, however.

“We’re cognizant of the fact that fishermen need some level of continuity,” Fleming said.

The groups haven’t specifically laid out the changes they would propose, but would like generally to see the permitted overall fish mortality for these five populations drop below levels that biologists consider sustainable.

Stricter rules wouldn’t necessarily require further decreases in the number of days of fishing allowed. Rather, “surgical” regulations, such as closing areas when the struggling species are known to be present, could provide innovative solutions, Fleming said.

Craig Pendleton, a Saco groundfisherman and spokesman for an industry group called the Northwest Atlantic Marine Alliance, worries that federal fisheries regulators will take the easiest route and decrease fishermen’s access to the resource across the board, he said Wednesday.

Fishermen catch many species simultaneously, so writing rules to protect a single fish population is challenging, he said.

Additionally, new restrictions on American plaice (which are known locally as dabs) and white hake will take a heavy toll on Gulf of Maine fishermen, who rely on these species and believe that federal scientists have substantially underestimated their numbers, Pendleton said.

“That’s what could kill us here in Maine,” he said.

Now Gladys Kessler, a U.S. federal district judge in Washington, D.C., will have the option of revisiting the case to issue her judgment of whether Amendment 13 meets the criteria of federal fisheries laws. Kessler can turn down the request, but CLF and NRDC have a new complaint ready to file if she does, so Amendment 13 will most likely face legal review in coming months.

Northwest Atlantic Marine Alliance and another fishermen’s group from Cape Cod had both intervened in the original lawsuit, and both would like to have input into any new rules but fear they can’t afford another year of legal wrangling, he said.

“This has been my worst fear all along – I’m in a sticky situation,” Pendleton said. “We don’t have any money left.”