A report by state Comptroller Thomas P. DiNapoli released April 6, 2016 showed that MTA figures underestimated average wait times for trains. View Full Caption DNAinfo/Rachelle Blidner

NEW YORK CITY — Creative calculating by the MTA misled riders about just how late the trains run, according to a new audit released Wednesday by the state Comptroller Thomas P. DiNapoli.

“The MTA is very clear that it considers its wait time assessment to be its most important measurement of the reliability of subway service and riders’ experience,” DiNapoli said. “It turns out the way Transit calculates this measurement obscures the reality of straphangers’ wait times.”

While MTA data has shown that wait times are up, the audit reveals that reality is even worse than previously reported.

The MTA uses a method called a wait assessment to measure the train’s ability to meet goals for the length of time between trains. That figure is found by averaging together the average wait times of all of the 23 individual subway lines and shuttles. But the problem is that this system equally weighs little-used lines like the Franklin Avenue Shuttle, which met its wait-time goal 96.2 percent of the time, with major lines like the 5 train, which met the wait-time goal just 68.3 percent of the time. This has led the MTA to find more optimistic wait assessments than riders actually experience.

Overall, the wait time got worse on 16 lines (1,4, 5, 6, 7, A, B,C, D, J, Z, L, M, N, Q, R) from January to December of 2015, compared to September 2013 to August 2014. Only five lines (2, 3, E, F, G) had better wait times in that period, according to the comptroller.

The MTA criticized the Comptroller’s report.

“Unfortunately, a recent audit from the Office of the State Comptroller includes misunderstandings, misinterpretations and outright misrepresentations of how the MTA is meeting these challenges, and is bereft of any substantive suggestions to make life better for subway customers,” MTA spokesman Kevin Ortiz said.

Meanwhile, riders kept asking tough questions on social media.