At a Tuesday meeting of the Connecticut Finance and Transportation Committee of the Legislature, Office of Policy and Management Secretary Robert Genuario said he made a mistake in managing a 15-year Department of Transportation plan for a New Haven rail-maintenance facility complex — which has turned out to be between $450 and $825 million more expensive than originally estimated.

“If I had it to do over again, I would have brought you into the loop early,” Robert Genuario told the committee.

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The admission follows four years of conflict between Gov. M. Jodi Rell and the Department of Transportation. On Monday, Rell ordered the OPM — a department of analysts who answer to her — to pay for an independent contractor to scrutinize the current construction plan, which state officials said costs about $762 million.

Genuario said at the meeting that there is a $250 million hole in funds to continue with the proposal. The DOT commissioner H. James Boice said the costs follow a “natural evolution” in projected budget increases for the proposal, first made in 2005, the Independent reported.

The OPM will judge the design and scope of the proposal and will make necessary cuts to the plan’s current proposed budget to “ensure only what is needed will be built,” according to a press release issued by the state on Monday. The current plan features numerous additions to the original plan, including a parking lot for employees and a walkway for workers to cross the wide set of railroads.

The OPM and DOT are currently in meetings, Rell spokesman Rich Harris said, but no formal changes have yet been proposed by Rell’s staff.

The review — which will be “as independent as possible,” according to the Monday press release — currently does not have a deadline set for completion, which some state officials said will cause an indeterminately long delay.

State officials from Rell’s office said the cost-cutting is simply a standard procedure intended to make sure all state departments spend tax dollars efficiently. Other state officials said they are concerned with the proposal, which can no longer work if the budget stays the same.

“I am understandably concerned about the increased costs,” Rell said, “and so are legislators.”

Genuario said he should have publicly addressed the ballooning budget earlier, according to the New Haven Independent. He continued to say that the original $300 million estimate for the proposal was unreliable because it relied on dated reports and did not adjust for inflation.

Harris said the state wanted to take another look at the proposal to see whether it could be executed with a cheaper budget. Current estimates for the project’s budget place costs at $762 million, Harris said, but the New Haven Independent reported that a March 2008 estimate put the budget — with inflation adjustments due to the 15 years the plan will take — at $1.17 billion.

“We cannot allow projects like this to expand and their costs to blossom out of control,” Rell said in the press release.

At Tuesday’s meeting, a number of state officials blasted the DOT and the latest proposal, calling it poorly planned.

“What we’ve learned today is that, for literally for years, the top administrators of the Rell administration have known that they were hundreds of millions of dollars short and yet they never disclosed that to the legislature,” said Sen. Andrew McDonald, D-Stamford, whose district includes many MetroNorth commuters. “And even as we stand here today, they still don’t have a plan of action.”

Plans for the New Haven rail project have been in the works since 2002. But plans for the site — located near the Union Street station — were formally proposed in 2005. By the end of 2006, contractors for the state had erected a $33 million Running Repair Shop facility for the railroads, but by then, the proposal had ballooned to include plans for a fueling facility, a power-supply station and more maintenance shops. Since then, the construction has been on hiatus while the proposal was being modified by the DOT.

Now there is an even longer delay. It remains unclear, Harris said, when the independent contractor will finish analyzing the plan — or when the OPM will even find a contractor.

The announcement follows years of tensions between the Rell and DOT — which has changed leadership three times in the last year. Earlier this year, Rell suggested splitting the DOT into two separate departments — one for highways and the other for public transportation — but talks of the proposal have since been quelled.

DOT representatives did not respond to multiple requests for comment through voicemail Tuesday. City Hall Spokeswoman Jessica Mayorga relayed comment to Transportation Director Michael Piscitelli, who was unavailable for comment because he was away from the office, a representative said.

Also in the press release, Rell announced that she has ordered Boice to review all other DOT capital projects to determine the cause of any budgetary changes.

—The Associated Press contributed reporting.