The number of major felonies in the subway system dropped in February for the second straight month, according to NYPD stats shared Wednesday — but MTA leaders say subway crime continues to be a problem.

February saw 104 major felonies, compared to 114 in January and 118 in December, according to NYPD Transit Bureau data. At the same time, all but two felony categories saw month-over-month drops in February — with the exception of murder, which increased from zero to two, and robbery, which jumped from 30 to 34.

Overall major felonies were down 62.5 percent year-over-year, Transit Bureau Chief Kathleen O’Reilly told board members.

But MTA officials — who called for and received an increased police presence following attacks on transit workers and a violent A train stabbing spree last month — said the numbers only tell part of the story, and defended deploying more cops on the subways and buses.

“I’m always gratified to see numbers going down, but you know, I’m always aware that one-off numbers don’t tell the whole story. I want to see all the numbers go down consistently, all the time, ” Interim Transit President Sarah Feinberg told reporters after the meeting.

“I’ll leave it to the police and others to comment on whether they think numbers have improved because of the police presence,” she said. “Certainly seems that way to me, but I would leave it to them.”

MTA Chairman Pat Foye noted that while crime was down 62.5 percent year-over-year, ridership was down by more — 65.8 percent, according to the MTA’s website.

“In the categories of crime that’s down, ridership is down by an even greater percentage,” Foye said.

“New York City and the region’s recovery is going to be dependent on a safe and secure transit system — that’s subways, buses, Metro-North and Long Island Rail Road.”