SEARSPORT, Maine — The U.S. Environmental Protection Agency has recommended that the Army Corps of Engineers reject Sears Island as a wetland mitigation site, complicating the state’s plan to balance conservation with development of a cargo port on the small island in Penobscot Bay.

In a letter sent to the corps last month, Carl DeLoi, chief of EPA’s wetlands and information branch, said the Maine Department of Transportation’s proposal to use the island as a mitigation bank was a problem. Mitigation banking is a procedure that instructs agencies to restore or enhance wetlands where possible and “bank” that acreage against future development on other wetlands.

DeLoi said the agency determined that the state’s plan failed to address aquatic resource restoration and would cause harm to the island’s long-term ecological integrity. The corps is the federal government’s deciding agency on wetland mitigation.

Maine’s Department of Transportation wants to use the 601 island acres it recently placed in a conservation easement as the mitigation bank. If approved it would be the first mitigation bank in New England. DOT wants to use the rest of the 930-acre island as the site of a cargo port. EPA contends that the two distinct uses would not mix well together.

“Notwithstanding our general support [for mitigation], this Sears Island proposal presents several concerns that make it a difficult choice as New England’s first potential compensatory mitigation bank,” DeLoi wrote. “As the prospectus is currently written, EPA recommends that the Corps not accept Sears Island as a suitable compensatory mitigation bank.”

Judy Gates, director of DOT’s environmental office, said the EPA comments were not unexpected and that the state planned to file a formal response. She said the letter was part of the process in pursuing the umbrella mitigation blanket and that each agency involved would submit comments on the proposal. She did not think the EPA’s move would scuttle the plan.

“I would expect [EPA] to be looking out for their own organizational mandates. It doesn’t come as a surprise,” Gates said Thursday. “We believe strongly in the ecological value that comes with mitigation banks. We’re working with them, not against them.”

Although in place elsewhere in the country, wetland mitigation banks are not in place in New England. DOT’s proposed bank would enable it to use land within the preserved acres to balance any disruption to wetlands or the marine environment that might be caused by port development on Sears Island.

DeLoi said EPA had determined that the DOT proposal for the protected area contained “little potential wetland or other aquatic resource restoration, approximately 2 acres at most.” Because only about one-quarter of the other 599 acres were wetlands, the proposal would not meet the national goal of “no-net-loss of wetland ecological functions,” the agency determined.

DeLoi said the proposal to develop a marine cargo port created a “high degree” of uncertainty over the long-term ecological integrity of the island. A cargo port likely would be a “highly disruptive presence” on the island and result in habitat loss, noise, lighting, air emissions from ships and vehicles and storm water discharges.

“The overall ecological value of the compensatory mitigation bank site would be substantially diminished,” he said.

Corps project manager Ruth Ladd said the EPA memo was just one of many documents that will need to be reviewed before a final decision on the wetland mitigation bank is made. She said the documents, including those filed by environmental groups opposed to the proposal, would need to withstand the scrutiny of an Inter-agency Review Team, or IRT, as well as DOT. In addition, she said, the corps had yet to decide whether a public hearing would need to be conducted on the project.

“We need to review all of this and send it to MDOT and the IRT,” Ladd said from her Boston office Thursday. “Deciding what happens next will take some time. This isn’t going to happen next month.”

DeLoi said the EPA could support the proposal, but only under very specific conditions. He said the proposal would have to contain provisions to protect the island’s rare dune grasslands, some of which are in the area targeted for development. He said the boundary between the preserved acres and the port area needed to be ex-panded.

“In summary, we have substantial concerns about MDOT’s current proposal,” he wrote. “At a minimum we believe the prospectus must be changed … and even in that case we urge the Corps to proceed cautiously with its review as this compensatory mitigation bank prospectus is New England’s first.”

Kyla Bennett, a former EPA attorney now serving as director of the New England branch of Public Employees for Environmental Responsibility, or PEER, said the EPA study confirmed what her group had been saying all along about DOT’s Sears Island plans.

“Maine DOT’s mitigation bank scheme is a transparently feeble attempt to get the nose of a very large and smelly camel — a container port — under the tent flap,” Bennett said Wednesday. “Nothing about this plan protects wetlands. It merely offers a pretext for destroying what it purports to preserve.”