A major project to dredge Menemsha channel has hit a snag, missing its Jan. 31 deadline for completion and raising ire among Aquinnah officials over damage at the West Basin.

The unfinished dredging project will not resume until next fall, Aquinnah and Chilmark selectmen learned this week.

Bret Stearns, director of the Wampanoag tribe’s natural resource department who has helped coordinate the Army Corps project, told the Aquinnah selectmen he learned last weekend that work would be on hold. The Army Corps estimated that only about a quarter of the project had been completed by the Jan. 31 deadline, which marks the start of the winter flounder season.

The contractor, J-Way Inc. of Avon, Ohio, got a late start last fall when storms slowed the movement of a dredge north from Georgia. Since late December the dredge has been at work in the pond, pumping sand a mile and a half down the road to Lobsterville Beach in Aquinnah, which was damaged during Hurricane Sandy in 2012.

Army Corps project manager Craig Martin told the Gazette this week that a little more than 15,000 cubic yards of sand have been removed from the channel so far. He expected another 45,000 cubic yards at most to be removed next year. The fresh delay has raised many questions, including how the company plans to repair damage caused at the West Basin, where the dredge pipes emerged from the pond and excess water flow has reportedly eroded a section of the parking lot. Further damage was reported along the sides of Lobsterville Road.

“As they are pumping, water is just spilling out constantly,” Aquinnah police Sgt. Paul Manning told the selectmen. “It’s just a big washout, right down into the water, and it’s encroaching onto the end of the pavement.”

The selectmen on Tuesday were somewhat exasperated by the sudden turn of events.

“I was shocked as to how little movement there has been since the 31st,” selectman Juli Vanderhoop said, throwing up her hands. “They are done! With all of the stuff just sitting there on the beach. It’s just a little shocking.”

Selectman Jim Newman stressed the need to hold the company accountable for the damage to town and tribal property. “We both have to go after it,” he said, referring to the town and tribe. But the extent and location of the damage was still unclear.

Mr. Stearns had planned to meet with J-Way owner Alan Johnson and an Army Corps representative on Thursday to work out the repairs and a schedule for next year, but in an email to the Gazette, he said he had been unable to address all his concerns since Mr. Johnson was meeting with the Army Corps representative at the time. He added that no town officials had attended the meeting.

“I did get a chance to discuss . . . my desire to plant a vegetative border along the new sand adjacent to the existing dune,” Mr. Stearns said in the email. He added that both parties were open to making that possible in some areas before dredging resumes in the fall.

Reached by phone on Thursday, Mr. Johnson told the Gazette that a meeting with the Army Corps and local stakeholders had been postponed to later in the afternoon.

“I’m just going there to listen,” he said. “We have a contract to perform, and our contract is specific. Unless they change it, we will be coming back on the first of October to finish the dredging.”

The dredging itself will likely not resume until around Oct. 15, since Menemsha and Lobsterville Beach are popular fishing spots in the Martha’s Vineyard Striped Bass and Bluefish Derby.

Not all the recent damage was on land. The dredging had apparently undermined a wooden piling that was installed last year to re-mark the Aquinnah-Chilmark town line after the old marker was wiped out by ice last winter. Aquinnah town administrator Adam Wilson said the new marker had simply floated away. “We have yet to relocate it,” he said.

Chilmark executive secretary Tim Carroll told the Gazette that as of Wednesday he had received no communication from the Army Corps about the delay, although he said it had been clear for a while that the project would not meet the deadline.

The Chilmark selectmen briefly discussed the project at their meeting on Tuesday, agreeing to postpone their plans to establish an anchorage in the pond, where they have been anticipating an influx of boats as a result of the deeper channel. They also agreed to postpone the purchase of a new harbor boat to help patrol the waterway.

Chilmark selectman Warren Doty said Wednesday that his town has been left out of the Army Corps discussions surrounding the project. “We don’t know anything about it except that it’s on hold,” he said. “We are on the outside.” Despite their apprehensions, the Chilmark selectmen had hoped to use some of the dredge spoils to replenish Squibnocket Beach, where a major restoration project is in the works. “We were just going to have to store it for a period of time anyway, so if the dredge comes back in October, we could get our sand then,” Mr. Doty said. In addition to the Jan. 31 deadline for completing the work, the contractor’s right of entry with the town and tribe expires in mid-February. Mr. Johnson said he had asked for a six-week extension, but the Army Corps requested only three weeks, until Feb. 21. The state Division of Fisheries and Wildlife had recommended an extension of only three days.

Mr. Martin of the Army Corps said the request itself had missed a Jan. 2 soft deadline for submittal, since too little work had been done to anticipate a completion date. The request was filed with the state Department of Environmental Protection on Jan. 26, with a response three days later.

Speaking to the Gazette by phone Wednesday, Mr. Johnson cited some accounts that winter flounder have been largely absent from the pond for years, and argued that the project could still continue. “Politically, if someone wanted to get it done they could make a phone call and get it changed,” he said. “But that’s not my call.”

Mr. Martin, however, said there was no chance of an extension this year, since the DEP already has issued its decision. “We’d be essentially asking the same question a week later,” he said.

Meanwhile, J-Way will need to disassemble the pipeline and store it on the Island or send it to the mainland on a barge. Several large pieces of machinery will also need to be removed. Mr. Stearns said the company’s goal was to cut the pipe into as few pieces as possible for transport. Installing the pipes took several weeks.

Aquinnah public works director Jay Smalley said at the selectmen’s meeting Tuesday that in his experience similar projects often take longer to break down than to assemble. He suggested storing the pipe sections in the parking lot at the Aquinnah Circle.

“We will charge them for storage if we can,” he said. “I think that’s the perfect spot.”

Mr. Martin said the company has until Feb. 15 to clean up the site and relocate its equipment. He expected the Army Corps to decide in the next few weeks whether to terminate its contract with J-Way for default or invite the company back in the fall. He said it was the Army Corps’ first time working with the company, which had submitted the lowest bid for the project.

In any case, he believed the project could be finished in a single season. “It depends on when the contractor shows up,” he said. “But yes, they have more than enough time.”