FREEPORT — A comprehensive study of the town’s dwindling shellfish resources has been put on hold for at least another week and may be scaled back significantly or scrapped altogether.

On Tuesday, the Town Council balked again at spending money already appropriated for the project. The action came after several discussions on the topic in the last few months cited concerns about permitting.

Following an almost two-hour discussion with clammers in the audience about including the nearly $67,000 appropriation for the project in the fiscal 2014 budget, councilors could not reach a consensus and asked for more time to review a revised version of the project presented to them Tuesday.

This decision prompted the clammer spearheading the project, Chad Coffin, to send an email immediately after leaving the meeting, announcing his resignation from the Shellfish Commission.

“I think we certainly got the message tonight that the council has very little trust in the shellfish program and in our ability to get something done and done right,” Coffin said in the email. “I’ll send you my resignation from the shellfish commission (as soon as possible). I’ve put way too much of my personal time and money into this effort as it is and simply can no longer afford to do it.”

Councilors struck the project’s appropriation from the fiscal 2014 capital budget, which they adopted Tuesday. They scheduled a special meeting for April 30, where they will again discuss if they want to include it.

“I’m uncomfortable getting something tonight and then being asked to vote on it,” Councilor Kristina Egan said, adding that in general she is a proponent of the plan. “I want to make sure as we come out of this project, we have really good data.”

Three councilors were ready to spend previously appropriated money and provide funding for next year, including Councilor Scott Gleeson.

“We’ve been batting this thing around for a while now,” Gleeson said. “I don’t think another meeting is going to do us any good. … I think the project should start moving forward.”

One of the project’s immediate roadblocks is the need for a permit from the U.S. Army Corps of Engineers to lay strategic fencing around clam flats. The town will submit a permit application to the Corps within the next few days.

Town Manager Peter Joseph said he expects to hear back on the application in about three weeks, although Corps project reviewer LeAnn Neal said it could take up to 60 days, which could disrupt the scheduling of the project.

Without seeing the application, Neal said she could not comment on its likelihood of approval, noting that the main concern with a fencing project would be creation of an impediment for other species to navigate the waters.

If the permit is denied, the overall project would have to be scaled back. That led councilors to question whether equipment should be purchased if the scope of project could change.

The purpose of the project is to help discover what’s causing clam populations in southern Maine to disappear. Clammers and scientists working on the project hope the data will bring them closer to bringing back a resource they’ve seen in dramatic decline in recent years.

The Shellfish Commission, which is overseeing the project, originally hired Brunswick-based consultant Resource Access International to study the factors contributing to the decline of clam populations.

The consultant’s work focuses not only on the green crab problem, but also on other significant issues believed to be contributing to the decline of crabs, including ocean acidification and disease.

In coordination with that study, which is funded through a matching state grant, the commission also planned to launch a larger trapping and fencing campaign. The combined project is supposed to run from summer to the end of the year.

After reviewing the plans in March, the council delayed the appropriation and directed the commission to sync the two plans into a “hybrid.”

With the help of Brian Beal, a biologist and professor at the University of Maine at Machias, the commission combined the plans, and the result was presented to the council Tuesday night.

Beal, who has studied the problem for decades and is consulting on the Freeport study, said this project is different from others.

“This is something I’ve been doing since 1988. What that has shown is that green crabs can be deterred from areas, which allows more clams to survive and more clams to settle,” he said. “All my studies have been small-scale, not large like this one in Freeport, and that’s the innovative part of this study.”

Clammers are currently on a four-day work week before the summer season begins. If the project is delayed, the available volunteers may quickly disappear.

And while Beal is interested in the scientific aspect of the study, clammers like Coffin worry that if they don’t start taking defensive steps now, it will soon be too late to do anything.

“This is the greatest natural resource threat in the state and no one knows about it,” Coffin said on April 19 as he prepared green crab traps to drop into Harraseeket River bay. “If we can’t defend these areas, it’s really our last chance.”

Will Graff can be reached at 781-3661 ext. 123 or wgraff@theforecaster.net. Follow him on Twitter: @W_C_Graff.

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Freeport clammer Chad Coffin holds green crabs he caught with traps set in the Harraseeket River tidal area on Friday, April 19. Coffin resigned from the town Shellfish Commission on Tuesday, April 23, after the Town Council postponed appropriating money for a study to determine the impact of the predatory crabs on the clam population.

Freeport clammers Chad Coffin and Clinton Goodenow gather coordinates for a green crab fencing project in the Harraseeket River, Friday, April 19.

Chad Coffin throws a green crab trap into the waters of the Harraseeket River on Friday, April 19.