Commuters litter 13 bags worth of garbage a day at just one Queens subway station, a report said Tuesday.

The Flushing-Main Street stop is one of 39 stations where the MTA is testing the effect of dumping garbage cans, according to a state comptroller audit of that pilot program.

The report was critical of how the MTA measured the program's success before expanding it, and said it did not get enough feedback from riders through customer surveys.

The MTA started nixing the cans four years ago at the Queens stop and one Manhattan station to reduce the number of trash bags sitting at stations -- and to slash its resident rat population.

Before the project began at the Flushing-Main Street station, workers there took out 39 bags of garbage a day, the state comptroller audit said. It was not clear how much of that was litter and how much was in cans.

After the cans were nixed, 13 bags of trash a day were removed -- all rubbish from the station's platforms and stairs.

Despite the large amount, the MTA says stations without trash cans have less garbage lying around.

"Litter, measured by the percentage of stations with no or light litter in the morning and daytime, increased initially, but rebounded and improved later during the pilot and is currently on par with stations that have trash cans," said spokesman Kevin Ortiz.

"Stations with cans with no or light litter stand at 85% while stations in the pilot without cans are hovering above 80%. So, since litter at stations without the cans hasn't increased substantially, it shows that customers are taking it with them."

The audit, which looked at 10 stations in the pilot, said only one stop saw a decrease in rats -- while nine stations saw no change.

Nearly every stop chosen for the pilot already had the lowest ratings possible for rodent activity, the state comptroller's office said.

The audit also said that the MTA did not perform the promised customer surveys. o It noted as well that the MTA increased the number of garbage trains that run during the day in 2011, making it difficult to judge whether removing cans had an impact on how many bags sit on platforms.

"We wholeheartedly disagree with the comptroller's opinion," Ortiz added. "The less trash generated in the station, the fewer the bags to be stored, collected, and potentially exposed to customers. This also decreased the rodent population providing a better customer experience."