Subway riders are waiting longer for trains, and longer than the MTA would lead commuters to believe, according to a new report from State Comptroller Tom DiNapoli's office. NY1's Jose Martinez filed the following report.

Grab a seat, check your phone, get comfortable - the wait for a train could be long.

"They've been having a lot of track, signal problems and stuff like that. So I find that the timing is off," said one subway rider.

So does a new audit from state Comptroller Thomas DiNapoli. It says riders are enduring longer waits for trains on three quarters of the MTA's 21 major lines.

"Service has deteriorated. I don't think it's any big surprise to most of the riders waiting on the platform for a train that hasn't arrived yet," said Matt Sweeney, a spokesperson for the state comptroller's office.

The audit examined wait times, the MTA's targets for the number of minutes between trains.

The comptroller says in the first half of 2015, the MTA met those targets systemwide 78.4 percent of the time, a falloff from the previous year.

But DiNapoli says the MTA's measurement may make subway performance appear better than it is because the agency tallies each line’s average performance, treating puny shuttle service the same as longer lines like the A train.

"When they average in shuttles with something as major as the Lexington Avenue line, it raises the performance of the Lexington Avenue line," Sweeney said.

In all, 16 major lines saw an increase in wait times last year. Just five lines saw an improvement.

The worst performance was on the 5 line, which met its wait targets just 66 percent of the time.

This is the second time in eight months DiNapoli has criticized the MTA's performance. In August, he examined another MTA measurement and found it deteriorating: how often trains arrive on schedule at their last stop.

After responding forcefully to DiNapoli's earlier report, the MTA once again fired back at this report, saying it 'misrepresents, misinterprets and misunderstands' what the transit agency is trying to do to improve service."

The MTA says it continues to modernize signals so more trains can run and replace equipment to cut down on failures.

The agency acknowledged it's strugling to handle surging ridership, but that it's working to do better and added, "The comptroller's audit does nothing to help this effort."