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Commuters are taking longer, cheaper bus rides to avoid paying the steep LIRR and Metro-North fees within the five boroughs, the city Department of Transportation said Thursday at a hearing on transit-starved neighborhoods.

An express bus trip by a commuter from Rosedale, Queens to midtown Manhattan averages 83 minutes, Commissioner Polly Trottenberg said, while a comparable LIRR trip takes only a half-hour. The express trip takes more than double the time, many Queens residents won’t use the LIRR because the $10 rail trip costs $3.50 more than the bus.

“Many parts of the city with the longest commutes into Manhattan … like eastern Queens and the northern Bronx, have commuter railroads running through them,” Trottenberg said. “Lower-income city residents often choose express bus or faraway subway service due to the very high ticket prices for the LIRR and Metro-North.”

The City Council is considering legislation that would lower the cost of a rail ticket within the city to the cost of a subway or bus swipe. The MTA said such a shift in its fare structure could cost it $70 million a year in revenue, according to written testimony.

“To remain financially whole, [the] MTA would need to be reimbursed for these discounts,” MTA chairman Thomas Prendergast said in written testimony. “Unfortunately, history has shown that we do not always receive reimbursement after we’ve spent the money.”

He noted that the MTA spends almost $540 million eachyear on Access-a-Rideand discounted MetroCards for seniors and students — far more than the city.

The former costs the MTA about $270 million on Access-a-Ride, compared to the city’s $180 million bill.The transportation authority spends about $267 million on subsidizing MetroCards, while the city pays slightly less than $40 million.

Councilman Ydanis Rodriguez appeared to be frustrated during the hearing, which addressed four bills and resolutions aimed to improve connections to “transit deserts.” Prendergast submitted written testimony for the hearing, but MTA officials were not there to take questions, which Rodriguez described as “irresponsible.” The city recently agreed to give the state authority $2.5 billion for its capital plan.

“We were invited on relatively short notice, and everyone who has any relevant experience and could give authoritative testimony was already committed to other things on their calendar,” MTA spokesman Adam Lisberg said.

Top MTA officials were also didn’t attend a Thursday morning Transit Wireless event on Wi-Fi at new Bronx subway stations, which was at the same time.

Councilman Ydanis Rodriguez said in the hearing that income inequality and access to public transportation are closely related, noting that almost a million New Yorkers commute more than an hour each way for jobs that pay less than $35,000 a year.

One bill he has introduced would require the DOT to study areas where there are no subway or bus stops a third of a mile from where the majority of a neighborhood’s residents live, along with areas where round-trip commutes often take more than three hours.

“The study would provide suggestions about how best to connect these communities … and would be done every five years as a way to measure our progress in improving the quality of life for these communities,” Rodriguez said.