Gov. Dannel P. Malloy was highly critical Wednesday of excessive and improperly authorized raises granted by Robert A. Kennedy, president of the Board of Regents for Higher Education, but he stopped short of saying he no longer had confidence in Kennedy’s leadership of the newly merged system.

“This was badly mishandled, inappropriately handled. It needs to be addressed. I’m happy there’s been an admission that this was wrong. But there’s going to have to be other steps taken,” Malloy said. “This whole thing has to be reviewed. I’m still gathering information. But you can be assured I’m not too happy right now.”

Malloy personally recruited Kennedy, the former president of the University of Maine, to assume leadership of a system merged at Malloy’s insistence. It includes the four campuses of the Connecticut State University system, the dozen community colleges and the online Charter Oak College.

“We gave him a charge. I wanted plans in place that allow students to move from institution to institution and drive up graduation rates,” Malloy said. “That plan is now in place. I wanted $5.5 million in savings by the consolidation. That’s been accomplished, so things have been accomplished, but this is improper.”

Kennedy answers to the Board of Regents, but Kennedy was the governor’s choice, and few would dispute that Kennedy could not remain as an effective leader of the system without the governor’s continued confidence and public support.

Malloy spoke to The Mirror at WNPR after he and Dan Esty, the commissioner of energy and environmental protection, discussed energy policy on the public affairs radio show “Where We Live.” He said he was unaware of the raises until The Mirror reported Monday that Kennedy’s executive vice president, Michael P. Meotti, received a $48,000 raise, which officials first released as $49,000.

“To give a $49,000 raise doesn’t fly. I’m not happy. I’m not happy I learned about it the same way you learned about it,” Malloy said. “And, quite frankly, it causes me to have questions.”

The governor addressed more reporters later Wednesday morning after touting his new energy policy at a South Windsor business. And while he again expressed frustration that he was unaware of the raises, he couldn’t guarantee others in his administration hadn’t been informed. Information about changes in compensation, job titles and duties typically also is shared with the governor’s budget office and the Department of Administration Services.

Were those agencies aware of the raises?

“I don’t have an answer to that to tell you the truth,” the governor said.

Two of Malloy’s top staffers, senior adviser Roy Occhiogrosso and general counsel Andrew McDonald, met Wednesday morning at the governor’s direction with Kennedy, Meotti and Colleen Flanagan Johnson, who is Kennedy’s chief of staff. She previously was Malloy’s communication director.

“It’s not complicated,” Occhiogrosso said. “The governor wants to know why what happened happened. How there could have been miscommunication on the issue of the college presidents? And how raises could have been awarded if they didn’t go through the proper process?”

The miscommunication issue refers to a community college president telling her faculty in an email that the presidents were facing termination if they do not accept a buyout, an interpretation higher education officials say is incorrect.

“The governor believes that people are human, and humans make mistakes,” Occhiogrosso said. “The governor’s position is when you make a mistake, acknowledge it, own up to it, apologize for it and do what you need to fix it. Andrew and I made those points to them this morning.”

Kennedy suspended the raises after the meeting and scheduled a late-afternoon press conference.

Malloy did take time in South Windsor to praise the Board of Regents’ system for achieving some budget efficiencies, making key investments in college campuses and expanding programs to meet a growing demand for workers skilled in precision manufacturing.

“They’ve done some wonderful, wonderful things,” he said. “They’ve done fantastic work, and then they go and screw it up, and I’m not happy.”

Meotti, a former state senator who was commissioner of higher education at the time of the merger, was Malloy’s choice to be the interim president of the Regents’ system. He remained as executive vice president after Kennedy’s appointment.

Meotti said Tuesday he would give up his raise, leaving him with a salary of $183,339. He was one of 21 Regents’ employees to receive raises between Dec. 20, 2011, and Sept. 21 on Kennedy’s authority.

But Kennedy acknowledged Tuesday he mistakenly granted the raises without a review by the Regents.

Occhiogrosso said the administration’s budget office had no role in processing or reviewing the raises.

“We don’t see paperwork for the higher education system,” he said.

Aside from the process, Kennedy will be facing questions about his political judgment for granting raises at a time when most state salaries are frozen, and the Malloy administration is struggling with a sluggish economy.

By inquiring more deeply, Malloy acknowledged, he will be taking ownership of a controversy generated by an autonomous public entity whose independence was repeatedly noted by the governor’s press office.

“I’m the governor. Governors get all the blame for anything that goes bad and not necessarily credit for good things,” Malloy said, mentioning the $5.5 million in savings.

“But this is a bad thing, and I’m not happy. It’s going to be dealt with. They’ve admitted they have to deal with it, but we’ll have other things to say about it.”

He is not alone.

Sen. Beth Bye, D-West Hartford, the co-chairwoman of the legislature’s higher education committee, who obtained details on the raises and top officials’ compensation, said she is pressing for more information.

“One of the missing pieces of information is, on what basis were these raises made? What additional duties did these employees take on to deserve such salaries?” she asked.

Bye said she was shocked at Kennedy’s compensation. In addition to a $340,000 salary, he gets a car, $20,000 in deferred annual compensation and $25,000 in expenses, according to the regents.

“It is disturbing to me that the Board of Regents’ central office seems to be operating on a completely different basis than most other state agencies, in terms of salary and benefits,” she said.

Bye said she wants Lewis J. Robinson Jr., the chairman of the Regents’ board, to meet with her and the committee’s co-chairwoman, Rep. Roberta Willis, D-Salisbury, and the two ranking Republicans, Sen. Toni Boucher of Wilton and Rep. Tim LeGeyt of Canton.

“There are many questions to be asked, and many expectations to be stated,” she said.

Keith M. Phaneuf contributed to this report.

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