Gov. Andrew Cuomo is having his way with the Metropolitan Transportation Authority again.

Amid the uproar surrounding allegations of overtime abuse there — uproar partly stoked by Cuomo — the MTA intends to hire a former federal prosecutor to look into the matter, in apparent deference to the governor and his closest ally on the MTA board, Larry Schwartz.

MTA executives plan to seek board approval later this month to retain Carrie Cohen, a partner at Morrison & Foerster who specializes in workplace misconduct investigations, according to several knowledgeable sources. As a prosecutor at the U.S. Attorney’s Office for the Southern District, she won the conviction of former Assembly Speaker Sheldon Silver. More recently, the New York City Council retained Cohen to investigate workplace misconduct.

Cohen did not respond to requests for comment. It’s not clear how much her contract will cost.

The MTA’s decision represents a victory for Cuomo and Schwartz, who encountered opposition when he called for tapping a prosecutor to look into overtime allegations at the MTA. It also represents the second instance in recent weeks of Cuomo and his allies installing an investigator at the transportation authority.

In May, the Senate approved Carolyn Pokorny, Cuomo’s former special counsel for public integrity, as the MTA’s new inspector general.

Though during her Senate hearing, she reportedly said it would be inappropriate to discuss ongoing investigations, her brief tenure has proven noteworthy for her willingness to discuss her own ongoing investigation into allegations of overtime abuse.

Cuomo and Schwartz have been decrying overtime abuse at the MTA ever since the Empire Center first reported in April that the authority had seen a 16 percent rise in its use.

“Including overtime and other extra pay, such as shift differentials, two transit employees earned more than the $325,600 annual salary of the agency’s president, Andy Byford,” the report noted.

MTA officials argued that aside from a few bad apples, much of the spike in overtime was due to the authority’s redoubled efforts to stop the system’s precipitous decline. Cuomo’s own MTA chairman said that he didn’t consider overtime abuse a widespread, systemic issue.

During an unusually dramatic closed-door meeting in May, some board members questioned the need for a former prosecutor to investigate overtime, given reports of investigations by federal prosecutors, the Queens District Attorney’s Office and Barry Kluger, Pokorny’s predecessor as MTA inspector general.

Ultimately, the MTA board decided it would hire a consultant instead. After the closed-door meeting, MTA Chairman and CEO Pat Foye told reporters that the consultant’s job would be to review “timekeeping and attendance processes and systems.”

The governor seemed to see that as a rejection.

“The MTA board and Polly Trottenberg and Pat Foye and all of them should have said, ‘We don’t need a consultant, we need a lawyer, we have zero tolerance for fraud,'” Cuomo said during an interview on WNYC’s “The Brian Lehrer Show.” “Do not presume that it’s a small handful, when you have no idea what you’re talking about. And that’s not what people want to hear. And it’s not what they deserve.”

As usual, Cuomo seems to have prevailed at the MTA.

“As discussed and agreed to at our May 22nd meeting, the board will be asked to consider a short term contract for a qualified outside party who can review issues related to time and attendance, as well as excessive overtime,” said MTA spokesperson Max Young.

A spokesperson for the governor said, “The [MTA] board made a decision to hire a special prosecutor and so we refer your questions to them.”

“This was all debated once and defeated,” said transit union leader and MTA board member John Samuelsen, whose union is in contract negotiations with the MTA, and who in May got into such a fierce war of words with Schwartz that some colleagues feared it would turn to violence. “This has now become an example of, ‘If I don’t get my way the first time, we’re going to ram it down throats anyway.’”

If, as expected, the board approves Cohen’s contract, her work is bound to overlap with Pokorny’s.

With the assistance of Gareth Rhodes, the former congressional candidate now on loan from Cuomo’s Department of Financial Services, Pokorny has publicly been investigating the overtime issue. The New York Post’s June 6 cover featured a photo of her holding purported evidence of time-clock sabotage. In June, her office created a Twitter account. All of her tweets have thus far focused on the governor’s bête noire: timekeeping at the MTA.

“New Yorkers have every right to know how their taxpayer dollars are being spent, and the Inspector General is committed to improving transparency and accountability and better educating New Yorkers how their tax dollars are spent across the MTA system,” said Michael Boxer, a spokesperson for Pokorny.

Pokorny’s apparent interest in publicizing the investigation runs counter to the office’s traditionally discreet behavior, and has inspired some skepticism among good-government advocates about her motivations — especially given the way her investigation seems to dovetail with the governor’s interests.

“We really hope IG Pokorny acts as an independent, career law enforcement professional, not a media grandstander politicizing her office at the governor’s direction during major labor negotiations,” said John Kaehny, executive director of Reinvent Albany.

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