Ultimately, Mr. Lhota said he knew the system was broken and he wanted to help fix it.
“I love a challenge, and anyone who knows me knows I love a challenge,” he said. “It ain’t going to be easy.”
Mr. Lhota is known for his outspoken style, from amusing Twitter posts about having sipped “too much wine” and his distaste for “Jersey Shore” to his contentious take that subway trains should not stop for kittens on the tracks, which prompted a Daily News cover reading “Die Kitties Die!” He is also a subway rider, using the No. 2 and 3 lines to travel from his home in Brooklyn Heights.
But Mr. Lhota now confronts a dire challenge: The subway is plagued by skyrocketing delays and fraying infrastructure. Long Island Rail Road commuters are facing a “summer of hell” as tracks are repaired at Pennsylvania Station. The sprawling transit network needs billions of dollars in repairs, and Mr. Lhota told lawmakers on Wednesday that fixing the subway would probably require even more painful disruptions for riders.
Business leaders and transit advocates welcomed his return.
Mr. Cuomo “has once again recruited an excellent leader for one of the toughest jobs in government,” said Kathryn S. Wylde, president of the Partnership for New York City, an influential business group. “Joe Lhota led the M.T.A. through Hurricane Sandy and is the right choice to lead the M.T.A. through the current crisis.”
The governor’s office said Mr. Lhota would continue to serve as a senior vice president at NYU Langone Medical Center and would receive an annual salary of $1 as chairman. A separate executive officer will handle the agency’s daily operations, a role Mr. Cuomo said he was still seeking to fill. The arrangement is a departure from recent years, when one full-time leader served both roles.
Mr. de Blasio threw his support behind Mr. Lhota on Thursday, saying he was the right person for the job when the agency was at a crossroads. Asked whether Mr. Cuomo was trying to “poke a stick” in his eye by naming Mr. Lhota, Mr. de Blasio said, “I think it has nothing to do with politics.”
“Joe Lhota and I ran against each other, but I have a lot of respect for him,” Mr. de Blasio said in a radio interview on WNYC.
But a few hours later, Mr. Cuomo turned on Mr. de Blasio, saying the city should pay more toward the M.T.A. and complaining that he, as governor, did not have the control he needed over the agency. Mr. Cuomo had proposed legislation to add two members to the authority’s board, whom he could appoint, but it failed to pass at the end of the session.
Though Mr. Cuomo has taken a hands-on role at the authority, he said the way it was set up made it unclear who was in control.
“Who’s in charge?” he asked reporters. “Who knows.”
Mr. Lhota’s appointment was a surprise, in part because he had said in January that he was not interested. In response to a Twitter post asking who would succeed the authority’s previous chairman and chief executive, Thomas F. Prendergast, he was unequivocal: “Not @JoeLhota. That’s a fact.”
Two other candidates had recently interviewed for the job: Veronique Hakim, the agency’s interim executive director, who would have been the first woman to hold the position, and Patrick J. Foye, executive director of the Port Authority of New York and New Jersey. Mr. Lhota said he respected Ms. Hakim and would consider her for the executive officer role.
Even if many were pleased by Mr. Lhota’s return, some criticized the lack of transparency by Mr. Cuomo, a Democrat, in naming him at the last minute. After Mr. Prendergast stepped down in January, Mr. Cuomo stalled on announcing a replacement, even as the system’s problems mounted. The State Senate confirmed Mr. Lhota as chairman around 11:30 p.m. on Wednesday, shortly before adjourning for the year.
In a hastily called Senate meeting Wednesday night, Mr. Lhota took questions from lawmakers via Skype. He noted that the subway runs around the clock and said that in order to replace the antiquated signal system — which dates to the 1930s and frequently fails, causing delays — officials might have to temporarily shut down lines, despite the hardship that would cause riders.
“If we want to get the signal system in as fast as possible, we’re going to have to do something like that,” he said.
State Senator Michael Gianaris, Democrat of Queens, said the late-night meeting offered little opportunity for public discussion and criticized lawmakers for failing to address the subway crisis.
“Better management is only part of the problem,” Mr. Gianaris said. “A lack of resources and historic underfunding is a huge part of the problem, and we did nothing to address that.”