A federal grand jury in Manhattan Tuesday returned a 14-count indictment of Joseph Percoco, a former top aide to Gov. Andrew M. Cuomo, and seven others on corruption charges in two wide-ranging bribery schemes to rig bids and wield influence on upstate development projects.

The 35-page indictment, which largely tracked a criminal complaint filed in September, accused Percoco of taking over $300,000 in payoffs to wield influence in Cuomo’s executive chamber, while former SUNY Polytechnic Institute President Alain Kaloyeros worked to rig bids on $850 million in development projects in Syracuse and Buffalo.

Cuomo was not charged with wrongdoing, but the indictment said Todd Howe, a former lobbyist involved in both schemes who is now cooperating with prosecutors, had been a close aide to both Cuomo and his father, ex-Gov. Mario Cuomo, and described Percoco as the governor’s “right hand man” and “gatekeeper.”

Percoco “was a high-ranking, senior and influential part of the Governor’s staff,” the charges said. “Percoco also had a longstanding personal relationship with the Governor and the Governor’s family . . . who coordinated access to the Governor and often spoke for him on a broad array of substantive and administrative matters.”

The governor, in a statement, acknowledged that the charges hit close to home — his father once referred to Percoco as a “third son” — and showed the need for more work on ethics in Albany.

“This is a profoundly sad situation for me personally,” he said. “Now the justice system must take its course, and any of those found guilty of abusing the public’s trust should and will be punished. Changes need to be made to restore faith at every level of government.”

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Barry Bohrer, a lawyer for Percoco, called the case “unworthy of prosecution” and said Percoco would plead not guilty. “This case is a real turkey,” Bohrer said. “We will knock the stuffing out of it at trial.” Kaloyeros’ lawyer did not immediately respond to a request for comment.

The grand jury alleged two overlapping schemes with common threads of “bribery, corruption and fraud.”

In the first, it said, Percoco took money — some in the form of a “low show” $7,500-a-month job for his wife — from an energy company and a Syracuse developer to wield influence on matters ranging from a power contract to a raise for a Syracuse executive’s son who worked for Cuomo.

Percoco, 47, of South Salem in Westchester County, was charged with two counts of extortion, and conspiracy to commit honest services fraud with Howe, Competitive Power Ventures executive Peter Galbraith Kelly, and executives Steven Aiello and Joseph Gerardi of Syracuse’s COR Development.

Percoco was also charged with conspiracy to commit extortion under color of official right along with “others known and unknown,” but the indictment did not name any of his co-defendants as co-conspirators, and a spokesman for the U.S. attorney would not elaborate.

In the second scheme, the indictment said, Howe was paid hundreds of thousands of dollars by two major campaign contributors to Cuomo — COR of Syracuse, and LP Ciminelli, a Buffalo construction company — and worked with Kaloyeros to give them advantages in bidding for major projects, including the so-called “Buffalo Billions” project.

A lawyer for Kaloyeros, 60, of upstate Slingerlands, who made an $800,000 salary at SUNY and oversaw state high-tech development projects, said he was innocent and would be vindicated on wire fraud and conspiracy charges.

“Dr. Kaloyeros has dedicated his life to training young scientists, developing cutting-edge research and attracting outstanding tech companies, economic development and jobs to upstate New York,” said lawyer Michael Miller.

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Lawyers for Kelly, 53, of Canterbury, Connecticut; COR executives Aiello, 58, and Gerardi, 57, both of Fayetteville, New York; and Ciminelli executives Louis Ciminelli, 61, of Buffalo, Michael Laipple, 51, of Orchard Park, and Kevin Schuler, 45, of North Tonawanda, did not respond to requests for comment.

The case was assigned Tuesday to U.S. District Judge Valerie Caproni, a former FBI general counsel who presided at the trial of former Assembly speaker Sheldon Silver.

No date has been set for the arraignment of the defendants.