Jay Walder, the M.T.A. chairman from 2009 to 2011, said in an interview that the cuts were necessary given the authority’s huge budget hole after the financial crisis. They were made as carefully as possible, he said, and should have been revisited when the economy bounced back.

“The difficult choices you make during a crisis aren’t necessarily the same choices you make when times are good,” Mr. Walder said.

Hurricane Sandy put an enormous strain on the system’s already fragile infrastructure, and the M.T.A.’s all-hands response to the storm saved critical pieces of the subway from damage — but it meant less time and resources for other, less pressing maintenance needs, current and former employees said.

There was also, in the midst of the financial crisis and just before the storm, a series of changes to the transit authority’s management structure that created confusion and needlessly set maintenance back, according to interviews with five former transit leaders.

In 2009, Howard H. Roberts Jr., then the president of the New York City Transit Authority, put a general manager in charge of operating and maintaining each subway line, essentially making lines their own stand-alone railroads. It was modeled after his reorganization of the authority’s bus system in the 1980s, a management structure that is still in use today.

Critics of the plan said it did not work as well on the subway because, unlike bus operators, subway operators are responsible for maintaining traffic signals and the tracks trains ride on. They said it caused confusion among maintenance workers in areas where multiple lines came together and that it sometimes led to arguments over whose line would pay for replacing key track parts.

They also said general managers prioritized running trains over interrupting service for time-consuming maintenance jobs.