The new Fulton Street Transit Center could cost another $15 million and fail to offer free transfers among the 12 train lines it is being built to connect.

The cost of the transit hub, which is set to open in 2009 and will connect the subways with PATH service and the World Trade Center site in Lower Manhattan, has already risen to $888 million from $750 million.

The Metropolitan Transportation Authority has not received approval from the Port Authority of New York and New Jersey to construct a passageway on Port Authority property between the R and W lines and the E platform, which would cost the MTA between $2 million and $5 million to construct.

The only backup plan, which would involve digging the connection beneath Church Street, would cost the MTA at least $15 million, the president of MTA Capital Construction, Mysore Nagaraja, told the authority’s capital construction committee during its monthly meeting yesterday. Board members criticized Mr. Nagaraja for not finalizing the deal with the Port Authority earlier.

Meanwhile, the MTA is pushing forward with its plans to recruit upscale restaurants and boutique shops to the 24,000 square feet of retail space at the transit center, raising eyebrows among critics who say the MTA is more concerned with street-level activity than with providing good connections underground.

As Mr. Nagaraja unveiled plans yesterday to add five new street entrances to the transportation hub, as well as 12 elevators and 10 escalators, he said the MTA chairman, Peter Kalikow, has yet to identify funding sources that will cover the cost of these improvements and other construction. “We’re proceeding with the assumption that the project is fully funded,” Mr. Nagaraja said.