The Metropolitan Transportation Authority on Wednesday agreed to discount LIRR trips within New York City by as much as 20%, while moving ahead with an unrelated plan to raise fares paid by Long Island commuters.

The MTA Board ratified the NYC Outer Borough Rail Discount plan, mandated by the State Legislature, despite concerns from Long Island Rail Road officials, board members and transportation advocates, who questioned the fairness of reducing fares for city riders already paying less than Nassau and Suffolk commuters.

The measure to discount those fares starting in May passed in a 7-2 vote at the Manhattan meeting, where MTA Board members separately approved an update to the authority’s financial plan. That budget assumes a 4% fare increase next year for LIRR riders, including those in Nassau and Suffolk.

MTA officials made their reluctance clear over the discount, a condition of the legislature’s approval of a congestion pricing plan creating new tolls for drivers in Manhattan to fund the authority’s $51.5 billion capital program.

Some Long Island commuters are also displeased.

Jeffrey Caparella, who pays $308 for his monthly LIRR ticket from Hicksville, said the measure is "not fair," and doesn't consider cash-strapped Nassau and Suffolk riders with limited commuting options.

"What about people from Long Island that can't afford the tickets either? We have no choice — no subways, no buses to get in to the city," said Caparella, 43. "The people who need it the most are taking the hit yet again."

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The discounts will be subsidized using funds from the congestion pricing plan that sets surcharges for taxis and other for-hire vehicles, and eventually will create new tolls for other drivers, in Manhattan. While the pricing plan commits 10% of generated revenues to LIRR infrastructure projects, LIRR officials said the discounts will cost them $16 million in lost fare revenues annually.

In a statement, MTA chairman Patrick Foye said he is "pleased that we will be able to leverage the MTA’s existing railroad operations to increase transit options and access within the City of New York for our millions of customers."

The measure aims to make the LIRR a more viable option for New York City residents living near a railroad station, but not near a subway line. It was the same motivation that led to the LIRR's "Atlantic Ticket," which discounted certain Brooklyn branch fares. Unlike the Atlantic Ticket, the discount program would lower LIRR fares at all times and for all stations in the city, except Far Rockaway.

With the discounts, unlimited ride monthly LIRR passes between any two stations within New York City will be discounted by 20%. Most other tickets within city limits on the LIRR, and its sister railroad Metro-North, would be discounted by 10%.

The discounts have supporters, who believe they will give city residents a needed transportation option.

"We're talking about working-class communities, far from subways, where people now have punishingly long commutes," said Danny Pearlstein, spokesman for the Riders Alliance, a nonprofit city bus and subway passenger advocacy group. "We believe it's fair to use existing infrastructure to get those people faster to where they need to go, and more easily. And part of that means bringing down prices to something that people can afford."

MTA officials emphasized that the pilot program would last between six months and a year. It would be closely studied to observe ridership patterns and capacity concerns.

Critics said those considerations could have been made ahead of the implementation of the plan, since they expect the discount may contribute to crowding and could send some Nassau commuters driving to catch a train in Queens for 20% less.

Commuters with the 20% discount would pay about $187 for a monthly ticket out of Rosedale, as compared to $270 out of Valley Stream, just 1.5 miles east.

Andrew Albert, a nonvoting rider’s representative on the MTA Board, said potential problems may be pronounced during the evening rush hour. "That's where you can have the possibility of people paying hundreds of dollars for a commutation ticket having to stand for people who did not,” he said.

Other board members expressed their reluctance on the discounts, including Neal Zuckerman, who noted that rail commuters traveling from the farthest points in the MTA system — for instance, parts of Suffolk County — are paying “untenable” rates. A Ronkonkoma LIRR commuter who has to get a station parking pass and an unlimited ride MetroCard pays $7,224 annually.

“I do not support the notion of separate discounts for separate groups,” said Zuckerman, of Putnam County, who voted against the proposal. “I’m telling you, those who pay the most cannot tolerate this anymore … It is too much of a burden.”

Long Island’s two representatives on the board voted in favor of the plan. Suffolk representative Kevin Law said he had a "fiduciary responsibility" to vote for the measure.

"The State Legislature directed us to provide this discount and we don't have the discretion to vote against it," Law said.