The Metropolitan Transportation Authority’s board sent a clear message yesterday to developer Bruce Ratner that he will have to increase his offer of $50 million in cash to gain control of the Vanderbilt Yards in downtown Brooklyn, where Mr. Ratner seeks to build an arena for his professional basketball franchise, the New Jersey Nets. One board member, Barry Feinstein, said the Ratner cash bid is “unacceptable” and noted that an appraiser hired by the MTA has assessed the yard’s market value at $214.5 million.

The board voted 13 to 1 yesterday in favor of a resolution proposed by its chairman, Peter Kalikow, instructing the MTA to negotiate the terms of the sale of the yards exclusively with Mr. Ratner’s firm, Forest City Ratner. It did not authorize the MTA to enter into talks with a rival bidder, the Extell Development Company, which offered $150 million in cash for the site.

In March, when the board rejected the higher cash offer in a similarly acrimonious battle for development rights of the MTA’s West Side rail yards, the spurned bidder, Madison Square Garden, took the transportation authority to court. An Extell spokesman, Robert Liff, said yesterday that his firm had ruled out the possibility of suing the transportation authority over the Vanderbilt Yards. A real-estate litigator who is a member of the anti-Ratner group Develop Don’t Destroy, Candice Carponter, vowed, however, to file a lawsuit on behalf of neighbors of the 8.4-acre rail yard whose homes would be seized through eminent domain under the Ratner plan.

Mr. Kalikow, himself a real estate developer, said it would be “immoral” to negotiate simultaneously with Mr. Ratner’s firm and Extell. “I have never sent two tenants a lease for the same space at the same time. It’s not right,” he said.

The board member representing Suffolk County who cast the lone dissenting vote, Mitchell Pally, argued that the MTA would maximize the sale price by negotiating with both firms at the same time.

One of the four board members appointed by Mayor Bloomberg, Susan Kupferman, said the city’s delegation wanted to approve the Ratner bid without modification, but the Bloomberg appointees joined in supporting Mr. Kalikow’s resolution once it became clear that they could not push the Ratner plan through at yesterday’s meeting.

An executive vice president of Forest City Ratner, James Stuckey, would not say if his firm is willing to increase its cash offer, but he predicted that negotiations with the MTA would produce a “positive outcome.”

In addition to the cash component, the Ratner package would pour a projected $189 million into the renovation of the MTA’s unsightly open-air rail yard, where the transportation authority currently cleans rail-car toilets and stores trains between weekday rush hours. The yard lies unused after dark, and the new fleet of M-7 trains, which cost the Long Island Rail Road about $1 billion, can be serviced on only one of the yard’s tracks.

The Ratner plan would cover the rail yard with a deck, add lights so that trains could be serviced at night, and lengthen the storage tracks to accommodate the M-7s. Mr. Ratner’s firm also pledged $29 million to build a series of passageways that would allow riders on 10 city subway lines to transfer to the LIRR without having to cross busy Atlantic Avenue.

Mr. Ratner also has said his proposed basketball arena would boost ridership on the MTA’s subways and trains because fans would take mass transit to get there. “Basically, the only thing that was missing from the Forest City proposal was the money,” one of Governor Pataki’s six appointees on the board, Nancy Shevell Blakeman, said.

On the sidewalk outside the MTA’s Madison Avenue headquarters, the board’s resolution drew cheers from black community leaders who support the Ratner plan, saying it would bring 2,250 units of affordable housing, 15,000 construction jobs, and 7,500 permanent jobs to Brooklyn.

The pastor of House of the Lord Church, the Reverend Herbert Daughtry, who led 140 demonstrators in a prayer Sunday on behalf of the Ratner plan, said he believes the marchers’ prayers helped bring about the outcome of the MTA vote.