Manhattan District Attorney Cy Vance’s new policy of not prosecuting most turnstile jumpers is hurting the MTA’s bottom line, New York City Transit President Andy Byford said on Wednesday.

“I think that has had an impact,” Byford said on WNYC radio. “It is a factor.”

Fare evasion has become a huge issue for the MTA, agency officials have said, and is contributing to the need to raise fares and tolls in the next few months.

Byford said he’s still crunching the numbers and should know what the cost is by the next MTA board meeting in a couple of weeks. Byford also said he’s not being “passive” about fare beaters and has assigned enforcement agents who usually monitor Select Bus Service routes to regular buses.

Vance loosened his policy on fare evasion earlier this year, telling cops he would no longer prosecute turnstile jumpers criminally as long as they pay a fine and stay out of trouble.

This isn’t the first time that MTA brass has commented that the new policy is causing the agency trouble. In February, former Chairman Joe Lhota called the lenient policy a burden.

“Fare beating places a burden on low-abiding transit customers who DO pay the fare, including low-income citizens who despite financial challenges, still respect the rule of law and their obligation to pay their way,” Lhota wrote in a letter to Vance at the time.

Vance’s office didn’t immediately respond to requests for comment.