As details emerge about the city’s redesigned effort to develop the far West Side, critics are saying that the proposal will saddle the MTA with hundreds of millions in cost overruns for the planned extension of the no. 7 subway line.

The issue of cost overruns for the $2 billion western extension of the no. 7 line — to outside the expanding Javits convention center from the line’s current terminus near Times Square — has been a point of contention between the city and the MTA since the Bloomberg administration proposed extending the line. City Hall has offered to pay for the entire project with proceeds from an upcoming bond issue but is driving a hard bargain on paying for any delays.

In the deal announced yesterday, the city would pay $2.1 billion for the subway extension, according to a statement issued jointly by the city and the state. That only allows $100 million for overruns in the $2 billion estimated cost of the project.

The deal could be approved by the MTA board as early as today.

A former chairman of the MTA, Richard Ravitch, told The New York Sun, “I think the MTA may have a significant dollar exposure that could adversely affect their credit.”

The attorney for the Straphanger’s Campaign, Gene Russianoff, said that the MTA is renowned for shattering budgets. He said that estimates for the MTA’s East Side Access project, linking the Long Island Railroad to Grand Central, have risen to $6.3 billion from $4.3 billion in two years. The MTA has also battled rising estimates for its Fulton Street Transit Hub and South Ferry projects.

City officials familiar with the pending agreement on cost overruns say that the city will still be responsible for cost overruns on land acquisition, a leading cause of rising costs, they say, and for any future design changes. They say the city’s liability could still exceed $2.1 billion.

In July, the city offered the MTA $500 million to consolidate its control over the Hudson rail yards, the vast undeveloped tract of land in Midtown West where the mayor envisions dense commercial and residential development.

In that deal, the city would have bought some of the air rights over the eastern half of the rail yards, and the entire western rail yards, in an attempt to increase the certainty that the area would be developed. But critics, including the frontrunner in the race for governor, attorney general Eliot Spitzer, said the offer was too low, and the deal fell apart.

Now, the MTA will retain the western rail yards and the money it generates from sales and leasing of future development. The city will pay about 50% more for the development rights on the eastern half of the yards. Initially, the city sought to buy 3.4 million square feet for $200 million. Now, the city will buy 2.25 million square feet for the same price.

Property taxes from the eastern and western rail yards will be funneled to the Hudson Yard Development Corporation, which will use the funds over about 30 years to pay off the bonds used to fund the subway extension and other infrastructure improvements.

Under the new arrangement, future private developers of the western rail yards, where the Bloomberg administration sought to build a football stadium last summer, can avoid the approval of the Public Authorities Control Board, according to city officials. The PACB is where the Jets Stadium was killed and the Moynihan Station project is being held up by the speaker of the Assembly, Sheldon Silver.

Instead, the area will be rezoned, and proposals must comply with development guidelines designed by the city and the City Council, and pass through the city’s uniform land use approval process. The speaker of the City Council, Christine Quinn, gave her full support to the plan yesterday.