The agreement will allow state road crews to completely overhaul the three-mile stretch over the next three months. But it may also help repair the rotten relationship between the Senecas and the state, which have fought for decades over issues like cigarette taxes and highway tolls.

The latest dispute centers on the tribe’s casino revenues, including more than $250 million that arbitrators this year ruled the tribe owed. That decision has been contested by the Senecas, who own and operate three gleaming gambling halls on tribal lands in Western New York.

Through all of these issues runs a common thread: the Senecas’ claim of sovereignty. And the stretch of Interstate 90 that crosses their land resulted in several confrontations with the state police during the 1990s. At one point, tribal protesters dropped burning tires off an overpass along the same stretch of road to show their displeasure at a planned state tax on cigarettes, long a lucrative business for the state’s tribes.

The deteriorating section of highway, part of the New York State Thruway system, has been blamed for blown tires and tie rods and all other manner of swerves and close calls. It prompted Representative Tom Reed, a Republican from Western New York, to call for an investigation by the Justice Department in August, saying that Mr. Cuomo was endangering public safety.

Mr. Cuomo, a third-term Democrat, has said that Mr. Reed was simply playing politics, and that he had feared sending state road crews onto the reservation and giving the Senecas an excuse not to pay the casino revenue.