Gov. Andrew M. Cuomo sought Friday to distance himself from Joseph Percoco, his former closest confidante, and the state university system, one day after a federal prosecutors indicted Percoco and eight others in alleged bid-rigging scheme that touched projects across upstate New York.

The governor said he wasn’t in charge of contracts of some of his most high-profile upstate initiatives and repeatedly insisted the State University of New York — not himself or his executive chamber — made all the decisions. He referred to Percoco as “this gentleman,” even though in the past he has described him as a brother and his father’s “third son.”

A day earlier, U.S. Attorney Preet Bharara announced indictments against Percoco, the head of SUNY Polytechnic and six contractors alleging that in Buffalo, Syracuse, Albany and Orange County bids were fixed to reward Cuomo campaign donors. Bharara said Percoco had “put the arm” on government officials to facilitate the scheme and advance the donors’ interests.

He also announced that Todd Howe, a lobbyist who at times worked for Andrew and Mario Cuomo, already reached a plea-bargain deal and pleaded guilty to eight charges. Howe represented many of the contractors named in the indictment and worked with Percoco and SUNY Poytechnic President Alain Kaloyeros to rig bids, the prosecutor said.

Cuomo said he “wasn’t aware of who some of these people were representing,” and SUNY “made all of the decisions.”

“No, I had no idea about anything contained in that complaint,” Cuomo told reporters in Buffalo.

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Asked if he wasn’t aware of what a “top lieutenant” was doing “right under your nose,” the governor interjected: “Not top lieutenant.”

The governor instead pivoted to say Kaloyeros had been at SUNY a long time and worked under “five governors.” Cuomo came around to say Percoco “has been a long time friend of mine and a long time friend of my family’s” but continued to point the finger at SUNY.

“The process was not run through my administration,” Cuomo said. “SUNY made the decisions on the projects.”

Cuomo acknowledged the charges were “very serious” and “breathtaking.” He also said “if the allegations are true,” then the accused will “pay the price.”

But he sought to push back against criticism from other lawmakers, watchdog groups and even the FBI agent in charge of the investigation that the indictments “tainted” his administration’s upstate revitalization efforts.

“We do thousands of projects,” Cuomo said. “And we’re talking about nine charges — which are serious — but they are nine charges. So let’s keep it in focus.”

Kaloyeros also faces separate state charges for allegedly conspiring with an Albany-area builder to rig a SUNY Poly dorm contract. He was arraigned Friday in Albany City Court and released on his own recognizance.