Joe Lhota, the former chairman of the Metropolitan Transportation Authority, stepped down from the position last year due to potential conflicts of interest with his outside gigs, a report revealed Tuesday — a different explanation to the one he and Gov. Andrew Cuomo gave at the time.

In his Nov. 8 letter of resignation — published Tuesday by Politico New York after a lengthy fight with the governor’s office to obtain it — Lhota told Cuomo that the state’s ethics watchdog, the Joint Commission on Public Ethics, found his positions with outside employers were “legally incompatible” with the gig.

“Recently, my appointment as chairman has come under question and scrutiny,” Lhota wrote. “JCOPE told me, as a going forward matter, my outside activities are legally incompatible with my obligations under the state’s Public Officers Law, and that recusal could not adequately cure or mitigate any potential conflicts in a way that would satisfy the standard set forth in the law.”

Cuomo’s office initially declined to release the letter under New York’s Freedom of Information Law, but eventually relented when Politico appealed, the outlet reported.

The two-time MTA chairman did not list the conflicts in the letter to Cuomo, but during his most recent stint, he was also chief of staff at NYU Langone Medical Center and a paid member of Madison Square Garden’s board of directors.

MSG sits atop Penn Station — a key hub for the MTA’s subway and Long Island Rail Road services — and discussions of the station’s future are intertwined with those of the arena.

Lhota’s letter provides a different explanation for his resignation than the ones he or Cuomo offered when he stepped down in November.

“The original understanding was he would just help out for a period,” Cuomo said during a radio interview on Nov. 11. “He fulfilled that commitment to me.”

Lhota said at the time he took the position with “the sole purpose of halting the decline of [subway] service and stabilizing the system for my fellow New Yorkers.”

“When I agreed to return to the MTA it was with the understanding that I would maintain my private sector positions and delegate day-to-day responsibility to a new team,” he said.

John Kaehny, the executive director at Reinvent Albany, which repeatedly raised questions about Lhota’s business dealings, blasted Cuomo’s office for its earlier explanation.

“The governor’s office, at the time of his resignation, completely mischaracterized his resignation,” said Kaehny.

“This letter shows that was completely untrue and that Lhota was basically forced to resign because of complaints to JCOPE.”

Cuomo spokesman Patrick Muncie on Tuesday referred questions about the letter to the MTA.