Officials at the state’s largest public college system face a multimillion-dollar deficit they need to close quickly.

This comes even after the Board of Regents approved a budget last month that community college presidents say has forced them to cut programs and increase class size. To balance that budget, officials also had to draw from the system’s rainy-day fund.

“It is safe to say [the shortfall] will be in the millions,” said Colleen Flanagan Johnson, a spokeswoman for the 100,000-student Connecticut State Colleges & Universities (ConnSCU).

The projected deficit became apparent two weeks ago when the state comptroller told public college officials that they will need to contribute more than they did this fiscal year to cover current and retired employees’ health and pension benefits.

In the fiscal year that ended June 30, ConnSCU was required to put aside 46 percent of its payroll to cover these costs. Next year, the system must set aside 54.7 percent. This means that for each $1,000 paid in salary and wages, the college system had to pay another $460 for fringes. That will rise to $547 in the current fiscal year.

The increase is primarily the result of the state’s long history of underfunding its pension obligations. Union employees are slated to get a 5 percent pay raise and non-union staff 3 percent next year, which will also contribute to increases in required pension contributions.

Officials at the University of Connecticut, which is run separately from the ConnSCU system, are also trying to determine how to close the deficit this large fringe rate increase created in their budget.

The community colleges and four Connecticut State Universities had been advised to budget for a 5 percent increase to cover fringe benefits, rather than the actual increase of 8.7 percent. Because of this, Flanagan Johnson said, they will have to take further action once the size of the shortfall is known.

That number is expected to be available before the end of the month, she said.

A spokeswoman for the University of Connecticut said the school will have an estimate by next week.

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