Mullan attributed the delay to the year or more the state spent negotiating with the community and investigating alternative locations for a 24-hour, 11-acre service yard for Green Line trains that the state wanted to put squarely amid the Inner Belt, a little-utilized industrial area. That seemed like a suitable location to the state because it’s something of a no man’s land and because part of the property was publicly owned. Locals objected for the same reasons — arguing that if the Green Line is to fulfill goals of getting people out of cars and encouraging new development around transit, then the Inner Belt should instead be readied for new housing, businesses, and amenities.

“This is, if not our top priority, one of our top priorities in the transportation world,’’ he said. “It is a good project, it is a worthy project, and it’s one that we’re committed to.’’

Jeffrey B. Mullan, the state’s transportation secretary and CEO, said supporters should not see this as a lack of commitment to the Green Line or a sign of financial woes.

Missing that deadline will make the project more expensive, because the state will need to come up with an air-quality-improving short-term alternative to the Green Line or face legal and community pressure. The project delay was acknowledged in an annual status report that the state Department of Transportation must file with the Department of Environmental Protection to update its progress on the Green Line and other Big Dig mitigation efforts, a list known as the State Implementation Plan. The 2010 report was filed Friday, and transportation officials began calling local leaders and stakeholders to alert them to the delay before the report landed at DEP.

But this delay means more than disappointing residents in an urban corridor bracketed by elevated highways and suburban-bound commuter rail tracks but served only by buses and cars. The state is legally bound to finishing the Green Line by the end of 2014, because it is part of a list of nonautomobile improvements it pledged to offset environmental impacts of the Big Dig, comply with the federal Clean Air Act, and avoid a lawsuit from the Conservation Law Foundation.

Expensive, complex projects get delayed all the time, and this one will run through the state’s most densely populated city (Somerville) and cost an estimated $954 million, 50 percent more than the state predicted just a few years ago.

Somerville and Medford residents waiting to swipe their CharlieCards and ride the Green Line must now wait even longer. State officials disclosed Friday that completion of the project — discussed for decades, put off by a succession of administrations, and planned in earnest for the past five years — will be delayed again, until at least October 2015.

The state ultimately agreed in May to relocate the yard, pushing it to the east edge of the Inner Belt, next to an existing 30-acre maintenance yard that serves MBTA commuter rail trains, though the plan would be more expensive and require some eminent domain takings. Officials said previously the maintenance yard debate would not delay the project, but when they prepared their annual report they realized they were wrong, Mullan said.

“I think it’s time well spent, because I think we’ve got a better project than we had,’’ Mullan said.

He said the state would work with the community on a short-term environmental alternative, like retrofitting local MBTA buses to use less fuel and release fewer emissions.

“It’s disappointing, because you want the Green Line to happen as soon as possible,’’ said Rafael Mares, a Conservation Law Foundation staff attorney for transportation and environmental-justice projects. “What I think is important is if there’s no way to avoid the delay that at least there’s appropriate mitigation and the community has a say in that.’’

Ellin Reisner is president of the Somerville Transportation Equity Partnership, which has spent years engaging the community and trying to hold the state’s feet to the fire. “On some level I’m not surprised, but I’m disappointed,’’ she said. “As someone who works as an advocate for this, you have to constantly be paying attention to the process to make sure it doesn’t get railroaded.’’

The state does not have the money in hand to build the project but is working on an application for the Federal Transit Administration’s New Starts program, to win half the funds. Governor Deval Patrick has said the state will make good on its commitment even if that application does not succeed.

Mullan said that is still the case, and the state is especially optimistic about winning federal money with changes looming for the scoring process. US Secretary of Transportation Ray LaHood has said New Starts will be redesigned to value “livability,’’ including economic development potential and sustainability; under the Bush administration, projects won or lost largely on a riders-per-dollar formula.

But advocates of greener transportation worry that the state has not moved fast enough to balance transit and bike projects with highway construction, and that it remains hampered by the massive debt burden from the Big Dig and political wariness over new taxes for transportation.