The former president of Connecticut’s merged public college system has returned $25,000 to the state, restoring his full, unvouchered expense account for the fiscal year, according to an email to the Board of Regents for Higher Education.

Robert A. Kennedy’s expense account was part of a larger compensation package — also including a $340,000 base annual salary — that drew strong criticism from leaders of the legislature’s Higher Education Committee.

Robert A. Kennedy

“As a result of my employment termination, I am enclosing a personal check returning the ‘business expense funds for 2012-2013’ which were included in my 9-20-2012 paycheck as taxable income,” Kennedy wrote in an email addressed to the “state of Connecticut” last week.

“I am turning Bob’s check over for processing to (Chief Financial Officer) Bill Bowes,” Steve Weinberger, the system’s vice president for human resources, wrote on Monday to the regents.

Kennedy received $50,000 in total compensation to cover unvouchered expenses during his 13-month tenure — $25,000 both in 2011-12 and 2012-13. The funds were to use at his “sole discretion” to “assist in fundraising, community outreach, membership and enhancing to the position of the Board of Regents,” according to his contract.

Sen. Beth Bye, co-chairwoman of the legislature’s Higher Education Committee, said it makes sense that Kennedy refunded the money.

“There’s no way he was entitled to that money. I don’t know why [the accommodations account] was paid up front anyways,” she said, adding that “it wouldn’t be a bad idea to know what this money is going towards, either.”

Rep. Timothy LeGeyt of Canton, ranking House Republican on the Higher Education Committee, said Kennedy “absolutely” should have returned those funds.

“It’s hard to talk about (the contract) in isolated factors, but it was too generous,” said LeGeyt, adding that several provisions of the compensation plan were excessive.

“As more details surrounding this contract and process are uncovered, the more troubling it becomes,” said Sen. Toni Boucher of Wilton, ranking GOP senator on the committee. “Moreover,  this type of language — allowing for a ‘blank check’ provision — is incredible.”

Other parts of Kennedy’s compensation package included $19,274 in moving expenses, $20,000 a year in deferred compensation based on performance evaluations, an inaugural $25,000 bonus, $4,343 for unused vacation time accrued and a $36,863 vehicle. He also billed gas mileage and parking expenses. Kennedy’s benefits were spelled out in a five-year contract negotiated by Gov. Dannel P. Malloy’s administration.

Kennedy, who was recruited last year by Malloy to lead a consolidated system that includes Western, Eastern, Central and Southern state universities, the community colleges and Charter Oak State College, resigned earlier this month following disclosures he unilaterally approved executive pay raises without board approval.

Those raises included a nearly $50,000 pay hike for the system’s executive vice president, Michael P. Meotti, who also resigned. Kennedy acknowledged that the raises, which approached $300,000, lacked political sensitivity coming at a time when most other state employees face a pay freeze and while college students face rising tuition and fees and declining financial aid.

Kennedy’s problems over the raises were compounded by legislative anger over the disclosure that he was absent from the central office for six weeks last summer, using a clause in his contract allowing time off for professional development to work remotely from a second home in Minnesota.

Another misstep included disclosure that the community college presidents were being offered “expedite[d]” separations, after the central office insisted that the presidents were not being offered a “buyout.”

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