The chairman of the City Council’s Transportation Committee is accusing the Metropolitan Transportation Authority of stashing hundreds of millions of dollars in a “slush fund” that is now being tapped to fund a Metro-North Railroad station at a new Yankee Stadium.

The funding question arose yesterday at a City Hall budget hearing, where MTA officials discussed plans to pay for the station by transferring $40 million from a scrapped project to extend the N subway line to La Guardia Airport. The authority canceled plans for the $645 million rail link in 2004 and used half of the funds to buy buses for the private routes it took over that year.

Of the remaining $322.5 million, little more than one-third has been allocated, leading to criticism from the chairman of the council’s Transportation Committee, John Liu.

“Why would you leave that money there?” Mr. Liu asked MTA officials at yesterday’s hearing, suggesting the authority had pulled the funds “out of thin air” to pay for the Metro-North station, a key element of the Yankees’ stadium project in the Bronx.

The existence of the La Guardia fund, Mr. Liu said, was inconsistent with the authority’s earlier claim that it could not afford to go forward with a scheduled renovation of 12 subway stations because of a budget gap in its current capital plan.

“That is absolutely unacceptable and unconscionable,” Mr. Liu said. “It smacks of having a slush fund on the side for the MTA.”

The MTA dismissed Mr. Liu’s allegation, saying that allocations from the La Guardia account were subject to approval from the authority’s Capital Program Review Board, which includes representatives chosen by state lawmakers and the mayor. “I would suggest the allocation and budgeting of those funds were absolutely transparent,” the MTA’s director of capital programs, Greg Kullberg, said at yesterday’s hearing.

The review board was set last night to approve the $40 million funding for the Metro-North station. The MTA’s executive board signed off on the transfer in April. In addition to the $322.5 million used to purchase the buses, the MTA has also allocated $70 million from the La Guardia project to build a new bus depot in Staten Island. The account has $212 million remaining, and Mr. Kullberg said after the hearing that the authority had no specific plans to spend it. The MTA had thus far dipped into the account for “high-priority, important” projects, Mr. Kullberg said.

An MTA spokesman, Timothy O’Brien, said he was unaware of any other discontinued project with available funds similar to the La Guardia rail link.