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ALBANY - ALBANY — Alain Kaloyeros, a former state university administrator who was indicted in state and federal corruption cases involving state economic development programs, is suing to get the state to pay hundreds of thousands of dollars in legal bills.

Kaloyeros, who until he resigned on Oct. 10 was president and CEO of SUNY Polytechnic Institute, filed suit against two nonprofit corporations associated with the State University of New York.

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He said that without state reimbursement of his legal fees, he “may be deprived of his chosen counsel at this critical time.”

At the time of his arrest, Kaloyeros had long been one of the state’s highest-paid employees. He made more than $880,000 at the nonprofit SUNY Research Foundation, which supports SUNY research efforts, and more than $378,000 at Polytechnic.

Kaloyeros, a physicist, was accused of wire fraud in a federal criminal complaint in September. He was later arrested for his role in one of the SUNY nonprofit companies, the Fort Schuyler Management Corp. The company handled state economic development projects now under federal investigation, including Gov. Andrew M. Cuomo’s signature jobs project known as the Buffalo Billion.

Kaloyeros also was charged by state Attorney General Eric T. Schneiderman for his role at the other SUNY nonprofit company, Fuller Road Management Corp.

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Schneiderman is investigating what he called bid-rigging involving SUNY Polytechnic that favored developers who were also campaign contributors to Cuomo.

Kaloyeros has pleaded not guilty to all charges. Cuomo has not been accused of wrongdoing.

Kaloyeros has kept his job as a tenured professor at SUNY, but said he is not being paid.

Kaloyeros is suing for that salary as well as for unspecified legal fees owed to the Manhattan firm Steptoe & Johnson since June 2016. He cites policies within SUNY that would continue the salary and pay the legal fees of any officer and board member of Fort Schuyler and Fuller Road Management companies in the face of legal action.

Kaloyeros said other board members and officers under investigation are receiving compensation for legal fees.

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Kaloyeros said the nonprofit companies created by the state advised him in May 2016 that there was a potential conflict for an unnamed law firm that was representing Fort Schuyler and Fuller Road as well as Kaloyeros until that time.

Kaloyeros said Fort Schuyler and Fuller Road Management corporations “recommended . . . that he retain new counsel and represented that they would continue to pay his counsel’s feels and expenses,” according to Kaloyeros’ lawsuit.

Kaloyeros said that compensation ended after he was indicted and his law firm is owed “hundreds of thousands of dollars in legal fees and expenses.”

There was no immediate comment from SUNY Polytechnic.

With Yancey Roy