[UPDATE BELOW] Back in April, New York City Transit President Andy Byford strenuously denied a report in the New York Times that he was on the verge of quitting his job over frustrations with the man who ultimately controls the MTA, Governor Andrew Cuomo.

"I love New York, I love this job, I believe in this system, I believe in this agency, and I’m here for the very long haul,” Byford said at the time.

But multiple MTA sources tell Gothamist/WNYC that Byford is expected to leave his job in June after a year and a half at the position. They say that Byford and some members of his staff have alienated longtime MTA employees, and that he is stymied by a governor who does not hesitate to intervene in agency business.

“Andy's a nice guy. Internally, people seem to like him,” one source wrote. “But I'm ‘feeling’ Cuomo is acting with Transit like Trump is acting w/US government. Very bull-in-china-shop. But the china is heavy.”

On Monday, Byford again denied that he was leaving.

“I love my job, I love New York, I love the views from the new apartment I just signed a lease on,” Byford wrote in a text message. “I am not going anywhere—not this week, not this month, not this year, etc. We are making great strides fixing our system, and I’ll be here until that job is complete.”

(It’s worth noting that just last year, Joe Lhota, the former chairman of the MTA, denied reports that he was on his way out, only to exit a month later.)

The governor’s office has balked at the estimated $40 billion price tag for Byford’s Fast Forward plan to revitalize the transit system, and the two have differed on the kind of technology that should replace the system’s aged signals. But the most consequential example of Cuomo’s willingness to override his appointee came when, at the 11th hour, Cuomo suddenly announced an entirely new plan for the L train tunnel repair project, which Byford had been leading.

Speaking at a community board meeting on January 8th, Byford said he had safety concerns and “wouldn’t be steamrolled” into rubber stamping Cuomo’s L train plans until an independent engineering team had conducted a safety review. “It will take as long as it takes,” Byford said at the time.

It took approximately one week for the Governor to remove Byford from the project and put Janno Lieber, President of the MTA’s Capital Construction division, in charge.

An independent review of the new plan never happened.

“I think that what the public is longing for at the MTA is knowing decisions are made not for political purposes, but by independent professionals, transit professionals, and I think Andy Byford has that reputation,” said Rachael Fauss, a senior analyst with the good government group Reinvent Albany.

Fauss recently wrote a 170-page report on public trust and the transit agency that identified Cuomo’s tendency to meddle “the biggest single problem with the governance of the MTA,” and noted that the governor’s fixation on larger projects comes at the expense of more mundane but equally crucial initiatives, like Byford’s Back to Basics plan that targets issues like routine maintenance and train speeds.

The last time Cuomo rode the subway was on December 31st, 2016, at the opening of the first phase of the new Second Avenue Subway line.

“There’s more to running the MTA than just the big projects, there’s the day-to-day work, and I think there hasn’t been as much acknowledgement of that,” Fauss said. “In fact, there has been a strain on the MTA because of hiring freezes and the reorganization plan, and there’s been morale issues.”

In April, the Times noted that Cuomo and Byford hadn’t spoken since January. Larry Schwartz, chair of the MTA’s finance committee and a former aide to the Cuomo administration, confirmed that Byford and the governor spoke during a conference call last month regarding ballooning overtime costs. MTA Chairman Pat Foye and Vice President Ronnie Hakim were also on the call, Schwartz said.

"They communicated with each other,” Schwartz said. “The governor communicates the same way with everybody. I consider all the conversations the governor has with people to be productive."

Asked to describe the tone of the conversation, Schwartz said the governor was “direct.”

“I don't see it as confrontational, I see it as being direct. He's trying to solve problems, trying get to the bottom of what's going on. So he asks tough questions and he's demanding of people," Schwartz said.

In response to an emailed list of questions about Cuomo's position regarding Byford, the Fast Forward plan, overtime issues, and his own subway usage, a spokesperson for the governor, Dani Lever, wrote, “We are busy working—we'll leave the conspiracy theories and gossip to others who clearly have more time on their hands.”

[UPDATE / 12:03 p.m.] WNYC's Brian Lehrer asked Governor Andrew Cuomo about this story this morning, and whether he had confidence in Byford.

"I hired Andy Byford. I interviewed him," Cuomo said, after referring to Byford and his counterparts Phil Eng and Cathy Rinaldi, who run the LIRR and the Metro-North, as "division heads." (Byford is the president of the New York City Transit Authority, which oversees the subway system and the bus system.)

"But the MTA is going through an overall transformation. The MTA needs to make major reforms," Cuomo said, before railing against overtime abuses.

"I’m not happy with the job the MTA is doing. The riders are not happy with the job the MTA is doing."

When Lehrer pressed the governor on whether he had confidence in Byford, the governor responded, "Look, I have confidence in Byford, Eng and Rinalidi. You have senior management that is above them and a board that actually runs it. And that’s where the issue is going to lie for the transformation."

Cuomo added, "But in terms of additional revenue, we have a $30 billion plan. It’s not what Byford wanted, it’s not what Eng wanted, it’s not what Rinadli wanted, it’s not what the board wanted. They wanted more money, more money, more money...I believe the MTA can do a better job with the billions of dollars they now have."

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