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Litter is bugging Brooklyn straphangers faced with subway stations barren of trash cans.

The artificial trash can shortage is a Metropolitan Transportation Authority initiative, which was first rolled out at the F and G station and the Brighton Beach Q stop in 2012 and has now taken hold at all but one of the J, M, and Z subway stations in Brooklyn — in an effort to make them cleaner. The measure is supposed to convince straphangers to hold onto their litter and lower rat populations, which some of the latest batch of affected commuters said is bonkers.

“The people eat their food on the train and then they throw the wrappers wherever,” said Maritza Figueroa of East New York, waiting for a train at Bushwick’s Myrtle-Broadway station. “They are not going to hold onto it until they get out of the station.”

Indeed, coffee cups, donut bags, and water bottles were among the pieces of detritus shoved under benches and piled around subway maps last Friday morning.

Another rider agreed that the initiative makes no sense.

“There are going to be rats regardless, so they should give us the trash cans back,” said Shantel Jackson, from Bedford-Stuyvesant. “People are messy and this is going to be a mess.”

Nevertheless, the transit agency is holding out hope that the removal of the garbage receptacles will cut off rats’ food supply and drive down their numbers along the elevated Brooklyn lines.

“The trash cans were removed as part of a pilot program to study how to reduce the number of exposed trash bags in the subway station and to control the rodent population in the subway,” Authority spokeswoman Amanda Kwan said.

The agency began the initiative in April and finished removing the containers from the 17 stations earlier this month, a representative said. This is the third phase in the agency’s study. In the first, which began in 2011, workers eliminated trash cans from two stops, one in Manhattan and one in Queens. For the second phase in 2012, the agency expanded its efforts citywide, including at Seventh Avenue and Brighton Beach.

The cans have not come back at those stations and some affected straphangers said it is a problem, though it has changed behavior.

“It is annoying,” said Fred Shenkman, who lives in Park Slope. “But I am always good and I hold onto my trash.”

Studies at those stations showed a 1/30th increase in litter, but also showed the average amount of trash removed from the stations dropped from 6.2 bags per day to 2.2 bags per day, the rep said.

Transit honchos have not changed how many employees staff each station and do not plan to, according to the agency.

The only Brooklyn J and Z station that still has its cans is Broadway Junction, where the L, A, and C also converge. Subway Poindexters want more time to examine whether to remove the repositories from the major transfer point.

This phase of the study is supposed to last until December.

Reach reporter Danielle Furfaro at dfurfaro@cnglocal.com or by calling (718) 260-2511. Follow her at twitter.com/DanielleFurfaro.