The U.S. Army Corps of Engineers said this week that it plans to go ahead with a major dredging project in the Menemsha harbor despite objections from the town of Chilmark.

The $1.95 million project calls for removing six feet of material from the channel, basin and into Menemsha Pond. Funding for the project comes from the $50 billion Hurricane Sandy relief bill passed in 2012. The channel is designated by the Army Corps as a federal navigation project.

The basin spans the towns of Chilmark and Aquinnah. Elected leaders in both towns, along with shellfish, harbor and natural resources managers examined plans for the dredging project over the past year. A study was commissioned by the Woods Hole Group that showed the dredging would have minimal impact on the bathymetry of the pond and shellfish. The Aquinnah selectman and Wampanoag Tribe of Gay Head strongly backed the dredging plan.

But in February the Chilmark selectmen pulled their support for the project, citing concerns about disturbance to shellfish beds, both wild and farmed, in Menemsha Pond. Harbor master Dennis Jason also opposed the project out of concern that deepening the channel would invite more large yacht traffic in Menemsha Pond.

In an April 7 letter to the towns and the tribe, the Army Corps announced its intention to go ahead with the dredging.

“Given the need to restore the federal navigation project to its authorized dimensions after damages from Hurricane Sandy, the Army Corps will continue to move forward with the planning and design of both the Menemsha . . . . dredging and jetty repair projects,” wrote Ed O’Donnell, chief of the navigation section for the New England district.

The Army Corps is also pursuing a separately funded $1.5 million project to repair the Menemsha jetties which were damaged during Sandy.

The National Environmental Protection Act requires the Army Corps to solicit comments for 30 days. The notice will be posted sometime “in the near future,” the letter said.

Chilmark selectman Bill Rossi said this week he hopes the Corps will hold a hearing on the Vineyard. “We were disappointed to hear that, I wanted to support the shellfishermen that were against the project,” Mr. Rossi said. “I wanted to respect their opinion and wishes and that’s how I voted.” The Chilmark selectmen have not formally discussed the letter yet.

Bret Stearns, the natural resources officer for the tribe, predictably had a different reaction. “I’m happy to keep working together to see this through,” he said. “We’re still committed to working with the towns of Aquinnah and Chilmark to take every effort possible to assure we have shellfish and access for the future.” Mr. Stearns and Tobias Vanderhoop, chairman of the Wampanoag tribe, both submitted statements to the Corps this week backing the decision. Mr. Stearns said Aquinnah plans to use sand from the dredging to rebuild the dunes at Lobsterville Beach.

Craig Martin, Army Corps project manager for navigation in the New England district, said the Corps believes the project is needed.

“We have two opposing views, somebody is going to be unhappy with us,” he said. “It was evident that Hurricane Sandy had impacted it and it was an opportunity for us to move forward to get the project dredged. It’s likely it wouldn’t have been dredged in another scenario for years to come.”

He said the time frame for the project will likely be in the fall, depending on other permits needed. They include a water quality certification from the state Coastal Zone Management and an environmental assessment under the National Environmental Protection Act.

“We were hoping to move forward with the project this fall, hopefully we can keep it on schedule,” Mr. Martin said. “It will really depends on the resource agencies and the commitment to getting the right permits.”

The jetty repair project is in the design phase, he said, and is expected to be completed next fall or winter. He said the timing may depend on the dredging project.