The removal of trash cans at some city subway stations has caused more track fires and more litter, the state comptroller said Tuesday.

The MTA removed the garbage cans in 39 of its stations in 2012, in what it said was an effort to reduce trash and rats. A state-comptroller audit in 2015 found that the program was just making a mess in those stations as riders threw their refuse on the tracks and platforms.

The office’s follow-up audit released Tuesday found that the situation hasn’t gotten any better.

“Removing trash cans appears to have resulted in more track fires and garbage at a number of stations,” said New York state Comptroller Thomas DiNapoli.

The new audit found that the MTA also hasn’t done what it can to clean up those stations.

The agency did replace trash cans in the mezzanine levels of seven stations where track fires had become rampant, the comptroller said.

But the MTA still hasn’t figured out how to keep riders from throwing garbage on the platforms and tracks or how to measure how much there is lying around.

The MTA also isn’t alerting riders in all of the stations that there are no trash cans there and to take their garbage with them.

“The clearest progress in the MTA’s pilot program so far is that they’ve returned garbage cans to some of the stations. Five years after they started this experiment, there’s still no evidence that it’s benefited riders by reducing trash or rats in stations,” DiNapoli said.

There are no garbage cans at nearly 40 stations, including the Eighth Street station on the R line, the Flushing-Main Street on the No. 7 line and all of the J/M stations that are above ground in Brooklyn and Queens.

The MTA did not immediately return requests for comment.

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