By Nate Raymond

NEW YORK (Reuters) - The president of State University of New York's Polytechnic Institute has resigned from his position after prosecutors accused him of engaging in schemes to rig bids for state-funded contracts, his lawyer said on Tuesday.

Alain Kaloyeros, who oversaw a grant application process for Gov. Andrew Cuomo's signature $1 billion Buffalo Billion economic development program, resigned nearly three weeks after federal and state prosecutors announced the charges.

"Dr. Kaloyeros resigned because he believes that the federal and state prosecutions recently filed against him are an unnecessary distraction for the good people working hard at SUNY Poly," Michael Miller, his lawyer, said in a statement.

Kaloyeros, 60, was among nine people whom federal prosecutors in Manhattan on Sept. 22 announced charges against for participating in a pair of corrupt and fraudulent schemes involving state contracts worth hundreds of millions of dollars.

Among those individuals was Todd Howe, a lobbyist and an ex-adviser to Cuomo who secretly had pleaded guilty to federal charges and agreed to cooperate with authorities.

Prosecutors said Kaloyeros, who oversaw a grant application process for Buffalo Billion and similar programs, and Howe, whom he hired to help develop projects, conspired to rig bids for contracts favoring two developers.

New York Attorney General Eric Schneiderman announced separate state charges against Kaloyeros and real estate executive Joseph Nicolla for bid-rigging involving three multimillion-dollar contracts.

Following the announcement of the charges, SUNY Polytechnic Institute suspended Kaloyeros, who had been among New York's highest-paid state employees. A spokesman for SUNY did not respond to a request for comment on Tuesday.

Miller on Tuesday said that his client "is innocent of the charges filed against him and looks forward to being exonerated when the cases have run their course."

(Reporting by Nate Raymond in New York; Editing by Steve Orlofsky)