Five months after terminating its contract with J-Way Southern Inc. of Avon, Ohio, the Army Corps of Engineers plans to work with the company again to finish dredging the Menemsha channel.

In a letter to Island officials last Monday, Army Corps project manager Craig Martin said an agreement to proceed with J-Way and its bonding company, U.S. Specialty Insurance, had been signed and all work will be completed by the end of January. “This solution is in the best interest of the government as it is the most cost and time effective option,” Mr. Martin said in the letter.

The dredging project has been a thorn in the side of Chilmark and Aquinnah since last year, when the contractor failed to meet mandatory deadlines to protect migrating winter flounder, halting work midway through the project. Later much of the equipment was left on the site, including a 1.5-mile pipeline along Lobsterville Road in Aquinnah that remained in place for months, obstructing traffic and drawing the ire of town officials. A parking lot at West Basin in Aquinnah was also damaged. The Army Corps terminated its contract with J-Way in May.

Now the contract has been renewed; staging for the project will begin this month and dredging is set to resume in November. “All in-water work is to be completed by the middle of January 2017 barring any significant weather events,” an Army Corps statement said.

In an email to the Gazette this week, Mr. Martin said working with J-Way was considered the best option since the company “was available and prepared to complete the project with equipment located nearby, and has an understanding of the local conditions and contract requirements.”

At their meeting Tuesday, the Chilmark selectmen discussed possible improvements to the project this time around, but had strong reservations about working with the company again. The selectmen have opposed the project from the beginning, among other things citing concerns about a potential influx of summer boaters in Menemsha Pond once the channel is deepened.

“It’s kind of shocking that they hired the same contractor they had so much trouble with,” selectman Bill Rossi said at the meeting. “You hardly ever see that happening.”

Executive secretary Timothy Carroll said the bonding company had taken ownership of the project when J-Way defaulted this year.

“The bonding company did something behind the scenes to bring J-Way back, and then the Army Corps is in the position of having to legally justify why the bonding company can’t pick anybody it wants,” he said.

The channel was scheduled to be dredged in 2014, but work did not begin until last fall.

The project is among 152 projects in the Army Corps North Atlantic division that were tagged for federal recovery aid after Hurricane Sandy in 2012; it will be among the last to be completed in Massachusetts.

J-Way removed about 16,000 cubic yards of sand last season, with about 45,000 cubic yards still to be dredged. As before, sand from the channel will be pumped onto Lobsterville Beach, which was severely damaged during Sandy. This time, however, the pipeline is expected to exit the channel through the Menemsha jetties (possibly crossing the west jetty in Aquinnah), rather than along West Basin Road, where the parking lot was damaged last year.

The town of Aquinnah voted in May to acquire West Basin Road from the state, although the transfer is still in progress. Town administrator Adam Wilson said this week that the use of a state-owned road may have influenced the decision to reroute the pipeline. “I don’t know if there was ever permission given by the [Department of Transportation] to allow the pipe to run along West Basin Road . . . . It might have been an oversight,” he said.

“It’s a common practice to just lay [the pipes] out over water,” said Bret Stearns, director of the Wampanoag Tribe’s natural resources department, who along with Mr. Wilson and Mr. Carroll discussed the project with Mr. Martin last Monday. “I’m sure it’s going to take some organization with the Coast Guard and with the municipalities to make sure that there is continued access for vessels.”

The Coast Guard put out a notice to mariners last week advising caution and low speeds in the vicinity of the dredging work. A floating pipeline in Menemsha Pond will be marked with lights and buoys.

Chilmark and Aquinnah have complained about lack of communication from the Army Corps, which maintains the channel for federal navigation. Mr. Carroll said he had sent a letter to the Army Corps asking for an on site supervisor to communicate with the contractor and with town departments during the project. He cited a number of issues last year, including reports of trash on the beach and a oil leak that went unrepaired since the oil was a natural variety. The dredge also knocked over a wooden pile marking the town line in the middle of the pond. (Aquinnah paid for its replacement this year.) Mr. Carroll said the Army Corps has agreed to hire a supervisor, although he did not believe it would be a 24-hour position.

“But just someone coming down every single day, or most days, will be a vast improvement,” he said.

Mr. Carroll also pressed for a formal kickoff on the Island, rather than by conference call, so that everyone involved would have a chance to meet in person. “We don’t have any idea who their staff is going to be,” he said.

The selectmen agreed to send another letter to the Army Corps indicating the town’s expectations, and to authorize shellfish constable Isaiah Scheffer to serve as a liaison between the site supervisor and the town.

“It would be wonderful if this were a well-run project,” selectman Jim Malkin said. “I have no confidence that it will be this year.”