Even in a subway system often cluttered with trash, it stood out: a whole slice of pizza left carelessly on the floor.

The slice found its way into the grip of an ambitious rat that dragged it down the stairs of the First Avenue L station in Manhattan early Monday. A video of the spectacle spread quickly online, amassing more than two million views on YouTube, and a star was born: Pizza Rat.

A day later, Thomas P. DiNapoli, the state comptroller, released an audit that questioned whether an effort by the Metropolitan Transportation Authority to reduce trash and rats on the subway was working. Mr. DiNapoli said that a pilot program to remove trash cans from some stations had shown little evidence of success.

“After four years, the best one can say about this experiment is that it’s inconclusive, except for the fact that riders have a harder time finding a trash can,” Mr. DiNapoli said. His office declined to comment on the video of the rat.

The authority has removed trash cans from 39 subway stations in recent years to encourage riders to take garbage with them instead of dropping it in overflowing trash cans and leaving scraps for rats to feast on. On Tuesday, the authority defended the program, saying it had reduced the number of trash bags collected at those stations.

“We wholeheartedly disagree with the comptroller’s opinion,” Kevin Ortiz, a spokesman for the authority, said.

Officials at the authority declined to comment on the video, but one noted that the station in question had trash cans and was not part of the pilot program.

Still, trash removal remains a monumental undertaking for the authority, and the pilot program is one way it has tried to address the problem. The authority says about 40 tons of trash are removed from the system’s 3,500 trash containers each day.

The video of the rat, posted by a comedian named Matt Little, showed just what the authority is up against: riders who have no qualms about casting aside food and other debris while aggressive rodents wait in the wings.

Mr. Little stumbled across the scene around 2 a.m. on Monday as he left a comedy show in the East Village with a friend. Rather than being put off by it, he said, he was “100 percent impressed” by the rat’s tenacity, and he pulled out his phone. After the rat carried it down a few steps and then ran away, Mr. Little said, he was not inclined to pick up the slice and throw it away before boarding his train to Brooklyn.

“I’ll be honest — I didn’t follow up with the slice,” Mr. Little said in an interview on Tuesday. “It was just in a rat’s mouth. We’ll let that stay where it is.”

For decades, the city has waged a war on rats with few signs of progress. The latest city budget included $2.9 million for plans to eradicate rodents by targeting so-called rat reservoirs where the animals gather.

In a city of eight million people, everyone has a rat story, said Gene Russianoff, the staff attorney for the Straphangers Campaign, a rider advocacy group that has opposed efforts to remove trash cans from stations. His happened once near midnight as he waited for an F train at Carroll Street in Brooklyn and a rat appeared 10 feet away from him on the platform.

“I did what any normal New Yorker would do,” he said. “I shrieked and ran up the stairs to the token booth area.”