In a sharply higher estimate than just a month ago, the Metropolitan Transportation Authority is saying it will lose $100 million this year from fare-beaters on buses and subway lines.

The estimate Monday from the MTA's transit division chief comes even as the New York Police Department has stepped up efforts to arrest passengers who skip out on paying fares.

The NYPD's patrol services bureau arrested 1,228 people for fare-beating between Jan. 1 and June 24, an MTA spokesman said on Monday, compared with 609 arrests in the same period last year. That represents a 102% jump in fare-beating arrests, which have risen in every borough except Brooklyn.

Speaking to the MTA's Transit Committee ahead of the authority's monthly board meeting, New York City Transit President Thomas Prendergast said projected losses from unpaid fares had increased sharply. An MTA official later said the new estimate was $100 million a year.

The MTA was recently publicly estimating its losses at $14 million a year.

Adam Lisberg, the authority's chief spokesman, didn't explain why the estimate rose so sharply. Representatives of the MTA have been in the field recently, observing passengers on city buses and subways. From those anecdotal findings, the MTA extrapolates the total amount of fare avoidance city-wide, Mr. Lisberg said.

Fare-evasion arrests on buses alone have risen 72% in the current year, the NYPD announced Monday. In a statement, Police Commissioner Raymond Kelly said the added arrests were due in part to the deployment of uniformed "impact officers" on city bus routes.

"Officers throughout the city assigned to Impact are conducting regular checks of city buses during their tours," Mr. Kelly said. "This increased uniformed police presence on buses has resulted in additional fare evasion arrest[s] and we believe deters other crimes in transit."

In addition, the NYPD uses plainclothes officers to deter crime in the city's transit system, including fare evasion.

Despite the high price tag, fare-beaters still represent a small fraction of the MTA's annual ridership of 1.6 billion, Mr. Lisberg noted. But the costs are significant. For instance, the revenue lost by riders ducking turnstiles and bus fareboxes exceeds $93 million—the annual savings the MTA reaped with a controversial round of subway and bus service reductions in 2010.

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