HALLOWELL, Maine — Down East Maine’s ongoing scallop harvest is about to go from bad to worse.

The Maine Department of Marine Resources announced Friday that much of Cobscook Bay is being closed to scallop boats through the end of the 2011-12 season, which runs through March. That ban takes effect on Monday, Jan. 2.

“It’s going to be a bleak season,” Pat Keliher, the acting DMR commissioner, said Friday. “In fact, it already is. But our research along the coast shows the resource is in very, very rough shape.”

The closure that takes effect Monday includes portions of the east and south bays. The eastern boundary of the off-limits area is a straight line between Birch Point and Grove Point. The western boundary runs between Mahar Point and Crow Neck.

During an emergency meeting Tuesday in the Washington County community of Whiting, Keliher heard from fishermen that there is no shortage of scallops in Cobscook Bay, but few are large enough to be legally harvested. Some of those attending demanded that areas that have been closed for the last two scallop seasons — waters that collectively represent about 10 percent of Maine’s scallop fishery — be opened this season, not next, as planned, at least for a few days a week.

That’s not going to happen, Keliher said Friday.

“If we opened up the closed areas now, we’d be fishing over a lot of juveniles, a lot of seed and a lot of sub-legal scallops,” Keliher said in a telephone interview. “We would see high mortality in order to harvest some legal-sized scallops. We have an investment in those closed areas, and we are committed to keeping them closed for three seasons.”

Keliher said he’s “very concerned” about the impact of the Cobscook Bay closure on the fishing community, but says the closure is in that community’s long-term interest.

“It’s quite a tightrope we are trying to walk, and we’re damned if we do and damned if we don’t,” he said. “We’re trying to balance the resource and the sustainability of the resource in a way that has a long-term positive impact.”

In announcing the latest closure on Friday, the DMR noted that Maine scallop landings have declined from a peak of nearly 4 million pounds in 1980-1981 to less than a half million pounds each year since 2001. DMR began dredge-based fishery surveys of the state’s scallop resource in 2002, with surveys in 2006 and 2007 indicating that Cobscook Bay had the highest scallop density in the state, by far. The 2010 survey showed Cobscook Bay to be the only area exhibiting relatively high scallop production in recent years.

Because of that relative abundance, the Cobscook Bay fishery has attracted more than 100 boats in some years, according to the DMR. During the last two seasons, a majority of scallop boats in Cobscook Bay landed at or near the 135-pound daily limit throughout the first three weeks of the season, with catches dropping off by January. That hasn’t been the case this season, which opened Dec. 17. By the third day of this season, fewer than half of 16 boats sampled by the DMR were landing at or near the daily limit, with a mean catch weight of 103.8 pounds.

“Scallop populations throughout the state, including Cobscook Bay, are at extremely low levels,” the DMR said in announcing the imminent closure. “The department is concerned that unrestricted harvesting during the remainder of the 2011/2012 fishing season may deplete a severely diminished resource beyond its ability to recover. Continued harvesting may damage sublegal scallops that could be caught during subsequent fishing seasons, as well as reducing the broodstock essential to a recovery. … Significant immediate conservation closures are necessary to reduce the risk of unusual damage and imminent depletion.”

Keliher said the DMR is committed to reopening next year the 10 areas already closed.

“We’re looking at doing it on a rotational basis,” he said. “We want to continue to improve the resource while allowing access to it.”

Although Keliher told those attending Tuesday’s emergency meeting that he would be meeting with Gov. Paul LePage this week to discuss options for addressing the dismal scallop harvest, that never happened due to schedule conflicts, Keliher said. Instead, Keliher discussed the situation with the governor’s staff.

The governor has the option of introducing emergency legislation that would open areas now closed to scallop boats, with approval by two-thirds of the Legislature. Keliher said Friday that won’t happen.

“All the benefits from keeping those areas closed would be lost,” he said.