BOSTON -- The MBTA is billions of dollars in debt and threatening fare hikes and service cutbacks. But Team 5 Investigates found many of the MBTA's major construction projects are over budget and years behind schedule. The overruns add up to many millions of dollars.

At the Kenmore Square station, crews are working on improvements that started four years ago and were scheduled for completion in 2007. Team 5 Investigates learned the end date is now slated for June 2009 and the project is almost 40 percent over budget.

Commuters were astonished by the overruns.

"We have so many public officials who keep talking about spending money wisely, and then you drive through Kenmore Square and you see this," said one T rider.

"There's obviously an issue with project management if they're so far behind like this," said another commuter.

Team 5 Investigates obtained the MBTA's construction records. Of the 19 ongoing projects, only three are on time and on budget.

The new Charles/MGH station is two years late, and 32 percent over budget.

South station renovations are running four years late and 38 percent over budget.

So far, Ashmont station improvements are 10 months late and 27 percent over budget.

Mattapan station's upgrade is a year and a half delayed, with 23 percent in overruns.

Team 5 Investigates' Kelley Tuthill asked the MBTA if upwards of $100 million in overruns was acceptable.

"I stand behind it," said Charles L. O'Reilly, the MBTA's Assistant General manager for construction and design. "Can we do better? Yes. But nonetheless we've incorporated extra work into the projects for good reason."

According to the records, the reasons include elevator modifications, permit delays and in case after case, unforeseen site conditions.

"In many cases we've incorporated work into the project that in hindsight should have been incorporated at the beginning," said O'Reilly.

The head of the MBTA Advisory Board said that's a major flaw in the T's standard operating procedure.

"These are the people who run the system," said Paul Regan, executive director of the MBTA Advisory Board. "They should know these challenges better than anyone because these are all known commodities. I think that better communication, better scoping, would go a long way to preserving those millions of dollars."

Many delays occurred because of concerns from communities that Regan said should have been addressed before construction began. Installing handicap accessible elevators at Copley Station has been fraught with controversy and overruns. The project is now on hold indefinitely after construction resulted in a crack in the historic Old South Church.

"We asked the T to put elevators in different locations so they would minimize, if not eliminate, the risk to the landmark buildings," said State Representative Marty Walz. "So here we are again with avoidable cost overruns and avoidable delays."

"We take exception to the fact that people predicted that there would be damage to the church," said the MBTA's O'Reilly.

But Team 5 Investigates obtained a letter from 2005 from leaders at the Old South Church to the T's General Manager, which said in part, "the risks to our building from the proposed excavations for an elevator on Dartmouth Street are unacceptable."

In many of these cases, the T is paying for past mistakes. A legal battle with the disabled over accessibility resulted in the T being forced to spend $300 million. In some cases, they had to redo projects already under way.

"We can always get better," said Gary Talbot, who filled a new position at the MBTA: Assistant General manager for Accessibility Issues. "We're learning all the time."

Going forward the MBTA told Team 5 Investigates there will be a new approach to project management.

"That's exactly what the general manager has told us to do," said Talbot. "Don't do it and then turn around and have to undo it afterwards."

In the meantime , some projects drag on, with no disability access, detours and constructions barriers, while the taxpayers' meter continues to run.

"There is no excuse in the sense that they have to be relentless in managing these projects," said Regan. "They don't have the money to waste."