“People were screaming; people were throwing up because the smoke was so thick,” Mr. Kopp said as he stood on a street corner above the 125th Street station. His shirt was covered in dirt from when he climbed off the train into the tunnel.

When the train derailed, Mr. Kopp saw sparks from what looked like an explosion.

“I thought, ‘This is it,’” he said. “I thought, ‘We’re going to burn alive in here.’”

There were about 800 people in the subway tunnel after the accident, and it took more than an hour for all of them to get out, according to officials.

Mr. Lhota said the smoke and fire reported by riders was the result of garbage on the tracks that was set ablaze in the crash. Asked by reporters how fast the train was going when it derailed, Mr. Lhota said that would be examined as part of the investigation.

For Mr. Lhota, who is days into a job he has held once before, the derailment was an inauspicious beginning. He had planned to unveil the new South Ferry subway station in Lower Manhattan on Tuesday morning but instead traveled to the scene of the derailment. The South Ferry station was flooded during Hurricane Sandy in 2012, and the authority had just completed $369 million in repairs to bring it back to service.

Gov. Andrew M. Cuomo, who controls the subway and has come under heavy criticism for the continual problems, has vowed to take emergency action to improve the system since it became clear that the antiquated infrastructure was failing. Mr. Cuomo did not visit the derailment site, as he did when a Long Island Rail Road train derailed in January; his office said he traveled on Tuesday morning to Albany, where he called a special legislative session to begin on Wednesday.