Later Thursday, Mr. Cuomo’s office released a new statement in response to questions about whether the governor supported Mr. Byford and his plan. Dani Lever, a spokeswoman for Mr. Cuomo, offered support for Mr. Byford — and a list of other top executives at the authority. “The governor looks forward to reviewing the report and supporting the M.T.A.’s new management team in their effort to overhaul and modernize NYC Transit and bring relief to riders,” she said. “Andy Byford, Joe Lhota, Pat Foye, Ronnie Hakim, Phil Eng and Janno Lieber are changing the M.T.A. and that’s why they’re there.”

Technically, Mr. Byford was hired by leaders at the Metropolitan Transportation Authority, the state-controlled agency that oversees the subway. But Mr. Cuomo, who has taken a close role in setting the agency’s priorities, interviewed Mr. Byford in person and essentially signed off on him.

In the past, Mr. Cuomo has praised Mr. Byford in public, though Mr. Cuomo has also pressed him to focus on a new signal technology that has not been used on any major transit system. Mr. Byford’s plan relies on a proven technology that has already been thoroughly tested in New York.

The authority’s chairman, Joseph J. Lhota, says Mr. Cuomo is simply trying to keep pressure on the agency to become more efficient. Mr. Lhota views his role as helping to protect Mr. Byford from the difficult politics surrounding the agency so that Mr. Byford can focus on running the system.

But the plan’s release was quickly overshadowed by political squabbling between Mr. Cuomo and Mayor Bill de Blasio, and criticism from the actress Cynthia Nixon, who is running for governor in the Democratic primary.

On Thursday, Ms. Nixon said Mr. Byford’s plan is exactly what the subway needed. “The question is, will the governor listen to the study that he himself has ordered?” Ms. Nixon said.

A day earlier, Mr. Cuomo had told reporters the plan could not succeed without Mr. de Blasio pitching in some cash. Mr. de Blasio said that fixing the subway was Mr. Cuomo’s problem because he ran it. An M.T.A. spokesman hit back, saying the city owned the subway and the mayor’s unwillingness to help pay for the plan had made it “dead on arrival.”