The city’s $34 million plan to build a waterfront park at Long Wharf was cast into doubt Sunday, when the Federal Highway Administration announced the project might not be eligible for an expected 80-percent reimbursement.

The state plans to demolish the historic former Yale boathouse — located on the harbor — in order to build the new Pearl Harbor Memorial Bridge on Interstate 95 in New Haven. The city’s plan, which includes building a replica of the historic Yale boathouse as well as shoreline restoration at Long Wharf, was supposed to be funded by the state in return for the harbor property and inconvenience to the city.

Although the Connecticut Department of Transportation earlier agreed to this plan, officials said last week the state’s funding is contingent on the 80-percent federal reimbursement.

New Haven Economic Development Administrator Henry Fernandez said he would have expected to find out about the concerns of the federal government and state of Connecticut in the earlier stages of the project.

“The Federal Highway Administration was certainly involved throughout the process and knew what our intent was,” Fernandez said. “We gave our approval and supported the plan, and if there was going to be any problem, they should have brought it up before this point.”

Fernandez said the city of New Haven views the shorefront park plan as an appropriate project that helps solve key problems raised by the construction of the highway bridge. He said if the federal government will not provide the funding, then he would expect the government to help New Haven find another source.

As project coordinator, the Department of Transportation is committed to assuring the project is eligible for 80-percent federal reimbursement as its primary source of funding, DOT spokesman Chris Cooper said. He said the eligibility of the boathouse replication for federal funding was always conveyed in the communications between the city of New Haven and the state, but he believes the city proposed a project of a larger scope.

“There is no reason the boathouse can’t be replicated as originally called for,” Cooper said. “But other elements of the waterfront plans such as the creation of parks and additional buildings are ineligible transportation expenditures.”

Karen Dubois-Walton ’89, the mayor’s chief of staff, said work on the project began between New Haven and the Department of Transportation during the administration of Connecticut Gov. John Rowland. Although both the governor and the commissioner have been replaced, the agreements made under that administration still stand, Dubois-Walton said.

“We believe we have a binding agreement, and I think the state would be in a difficult position to say that we do not,” Dubois-Walton said. “This goes to the credibility of the state government and speaks to the ability to work collaboratively on future things.”

New Haven officials plan to pursue this issue at the state and federal level. U.S. Rep. Rosa DeLauro offered to get involved with the federal Department of Transportation, while New Haven Mayor John DeStefano Jr. will be seeking relief directly from Connecticut Gov. M. Jodi Rell, Dubois-Walton said.

Fernandez said the city is not ready to give up on the Long Wharf project.

“We expect to fight hard for our position, hopefully in an environment where we can reach a satisfying agreement,” Fernandez said. “If not, we’ll cross that bridge when we get there.”