Fare evasion on subways and buses is soaring — but could be even worse than the MTA has reported, according to the agency’s watchdog.

An investigation conducted earlier this year and published Thursday by MTA Inspector General Carolyn Pokorny’s office poked holes in the agency’s bus and subway fare evasion data, which is based entirely on in-person surveys.

In a July 2 letter to the MTA’s buses and subways division, Deputy Executive IG Elizabeth Keating ticked off a laundry list of flaws in the MTA’s methodology — in particular, the limited reach of in-person surveys, which are conducted by a single person at a single turnstile or bus and, until recently, lasted just 30 minutes each.

“For fare evasion the true value is unknowable without doing an impossible 100 percent sample,” Keating wrote. “Both surveys may benefit from simplification to make data collection less burdensome and thereby improve the accuracy of the overall fare evasion estimates.”

Even with that relatively limited scope, the IG’s investigation found that quarterly surveys only covered, on average, 60 percent of the 280 places and times selected for study.

The also IG notes that survey workers at subway stations wear MTA uniforms, which could impact would-be evaders’ decisions.

A single worker on each bus, meanwhile, has to monitor two and sometimes three doors, often in crowded conditions, the report adds.

In an official response, the MTA said it has already made changes in response to the IG’s concerns. Surveys are now conducted in hour-long stints, and subway surveyors now travel in groups, which avoids the need for a uniform, the agency said. An effort is also underway to simplify survey categories.

The decade-old surveys have shown marked increases in fare evasion in recent years, up to 3.2 percent on subways and more than 20 percent on buses, according to the most recent data.

Agency officials say they lose $225 million annually to farebeaters, and have previously suggested that their survey methods were likely undercounting the scofflaws. In June, the agency and Gov. Andrew Cuomo announced an influx of 500 police officers to combat turnstile jumpers.