Labor leaders and a close ally of Gov. Andrew Cuomo dueled over the Metropolitan Transportation Authority’s bombshell examination of its soaring overtime tab Friday, trading barbs over the causes of the agency’s runaway labor costs.

The furious exchanges between the president of the MTA’s largest union, John Samuelsen — a non-voting board member — and Cuomo’s former top aide and longtime ally, Larry Schwartz, came just hours after the agency released the 61-page report.

The two have been at loggerheads for months over Schwartz’s claims that fraud helped push the MTA’s overtime bill to $1.3 billion last year.

“Despite his denials, he was on CBS News ranting and raving in an inappropriate, hyperbolic manner about abuse and fraud among transit workers,” charged Samuelsen, president of the Transportation Workers Union.

He was referencing a WCBS-TV interview where Schwartz said that “[p]eople need to either go to jail, they need to be prosecuted, and we need to collect the money that they stole from the taxpaying public.”

Schwartz was commenting on a string of stories in The Post that highlighted how some Long Island Rail Road employees billed for thousands of hours of overtime in a single year.

“Read the transcript and watch the segment,” an angry Schwartz fired back at Samuelsen. “If you’d read it, you’d know what you just said was a lie.”

“It’s not a lie,” Samuelsen retorted. “The appearance that there are problems with overtime were triggered by you — it’s at your feet.”

He added: “There’s blood on your hands because transit workers were assaulted in the aftermath of your accusations about rampant fraud, which you still have not produced a lick of evidence about.”

The sparring came amid a two-and-a-half-hour special MTA board meeting that examined the report it commissioned, which castigated the agency for failing to keep track of how much overtime it doles out.

However, the Morrison & Foerster audit also attributed much of the MTA’s ballooning labor costs to outdated labor work rules and poor management practices.

The MTA’s overtime bill has exploded by more than 50 percent over levels in 2014 as it struggled to fix ancient signals and years of deferred maintenance that caused the subway system’s on-time performance to crater.

It paid particular attention to the LIRR, which awarded overtime at a higher rate than any other MTA division — including its sister commuter system, Metro-North.

Reports from the Empire Center and The Post exposed how some LIRR workers clocked more than 3,000 hours of overtime in a single year, allowing them to triple their regular pay.

“I think it takes a little bit of courage to lay it all out there, soup to nuts,” said Linda Lacewell, a recent MTA board appointee and a longtime Cuomo aide. “It paints a very ugly picture, it’s a gross abuse of trust, the public trust.”