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New York's two biggest cities would lose $110 million a year in federal fare subsidies for rapid-transit systems if President Bush's budget is adopted.

The Niagara Frontier Transportation Authority would lose a critical $6 million of that amount if Congress approves that part of the president's spending plan for fiscal 1991.

Gov. Cuomo's office here said the loss of federal operating assistance would force the NFTA to increase fares by 40 to 50 cents a ride, if the system could operate at all.

While the White House has tried to kill operating assistance in the past, the Bush administration is trying a new political tactic to eliminate the expensive program.

The plan calls for barring aid for transit systems that serve more than 1 million people. That would cover the nation's 30 largest cities.

Brad C. Johnson, Cuomo's representative, said the president is trying to weave a congressional coalition to kill the program. In the House such a coalition could consist of suburban Republicans and conservative Southern Democrats.

Last year, in his proposed budget for fiscal 1990, Bush tried to bar fare subsidies for cities of 200,000 or more, but that aroused a strong coalition for mass transit aid. "The president is trying to narrow transit's base in Congress," Johnson said.

Rep. Henry J. Nowak, D-Buffalo, would not predict that Bush will lose this time.

"Our transit systems cannot absorb any more cuts," Nowak warned. He noted that Rep. Bill Lehman, the chairman of the House subcommittee that would deal with that part of the budget, is a Democrat Miami, Fla., which would be affected by Bush's proposed transit cuts.

Although the Democratic-controlled House has beaten back many administration attacks on transit aid, the jawboning between the White House and Congress has taken its toll on the program.

The NFTA, for example, received $6.095 million this year, down $56,000 from last year. The current figure, however, is about $1 million less than the NFTA received in 1985.

"Every year the administration goes after this aid, and every year we lose a little bit," said Vito Sportelli, NFTA grants director. "It continuously gets racheted down. There's an erosion in the program."

While $1 million would not have been considered as critical during the 1970s surge of federal grants, it is now.

The NFTA had to lobby for weeks to get the Erie County Legislature approve a $1 million stop-gap aid to keep the Metro Rail system operating. At a briefing, Transportation Secretary Samuel K. Skinner said federal aid meets only 6 percent of the transit systems' operating budgets in the 30 cities that would be affected.

In Buffalo, however, U.S. fare subsidies constitute 10 percent of the Niagara Frontier Transit Metro System's operating budget.

Passenger fares and fees for transporting students cover only 38 percent of the system's operating costs.

The rest comes from federal, state and local subsidies.

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