“The decision not to have the rail collected by a work train was a decision by management,” Mr. Samuelsen said. “It is oversimplifying the tragedy by calling it just human error on the part of the supervisors.”

The subway in Washington also stores rails on the tracks, said Dan Stessel, a spokesman for the Washington Metropolitan Area Transit Authority, but he cautioned that it was important that they be properly secured. Amtrak no longer allows for replacement rails to be stored in the track area on the Northeast Corridor, said Mike Tolbert, a spokesman for Amtrak. The practice is allowed on Amtrak routes outside the Northeast, although speed restrictions are imposed in those areas.

As subway delays have skyrocketed in New York, Gov. Andrew M. Cuomo, who oversees the system, has faced growing pressure to address the problems. On Wednesday evening, a group of transit advocates held another rally outside his office in Manhattan to urge him to “fund and fix” the subway.

Mr. Lhota, who was named chairman last week, said he was working to restore confidence in the system. The agency was to hold a competition on Thursday soliciting ideas from transit experts around the world about improving service — a proposal made by Mr. Cuomo last month. The authority is seeking ways to improve the subway’s antiquated signals and to quickly buy more trains; winning proposals could earn a $1 million prize.

Asked about the pressures of serving as chairman while still a senior vice president at NYU Langone Medical Center, Mr. Lhota said he planned to hire an executive director who would manage daily operations so that he could focus on the agency’s “strategic direction.”