As budget cuts deepen across the University, the administration is giving employees a little and finding ways to save a lot.

Managerial and professional staff are losing some of their paid time off, vacation days and vacation bonuses, but they are also gaining short-term disability coverage, which will provide support to staff members who fall severely ill or become injured and cannot work. Staff interviewed applauded the new disability coverage, and said that while the other cuts to their benefits are unfortunate, they are better than more layoffs.

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“If it’s going to save jobs, then I think it could be a good thing,” said Joanne Bentley, the business manager for the Chemistry Department, who said she had never seen such major changes to Yale’s benefits package in the 25 years she has worked for Yale. “But clearly, it’s going to have a pretty big impact for years to come.”

Between the new disability coverage and the loss of vacation, sick and personal days, the tweaks mark a major change for Yale’s benefits package, which has historically been considered among the most generous in the Ivy League. The amount of paid time off that Yale offers to its staff is among the Ivy League’s highest. But Yale was, until now, the only Ivy League school that did not provide a short-term disability coverage plan — a program Vice President for Human Resources Michael Peel said was established in response to the many staff members who asked for such a benefit in a 2008 workplace survey. The adjustments bring Yale’s policies closer to those of its peer schools.

Though five staff members praised the new disability plan, which provides pay and benefits to staff for up to 26 weeks and full benefits through the sixth week, they criticized the cuts to their paid time off and vacation days — a benefit that tends to be greater at universities and colleges than at corporations. At Yale, staff can currently spend nearly two months a year away from work, using their vacation, sick and personal days, as well as University holidays and recesses, and they can accumulate as many as 64 vacation days they can carry over from year to year.

Even with the cuts, Yale’s paid time off still ranks among the highest in the group of Yale’s peers, Peel said.

“This change strikes the right balance, reducing costs to help us avoid as many layoffs as possible, while giving us a stronger total benefits package,” he said Wednesday.

A cut to paid time off is never welcome, said Andrew Morcus, a facilities operations manager for the Faculty of Engineering. Even so, he had expected the cuts because of Yale’s financial difficulties, he said.

“Yale has always had a fantastic benefits package, and sooner or later that was going to get beat up on,” he said. “We are taking a beating, but it’s still better than what’s out there.”

Staff may be losing out, but the University is gaining: By curtailing the number of vacation days staff can accrue and keep, Yale will ultimately not have to pay for as many unused vacation days at the end of employees’ careers at Yale. Federal and state wage laws require the University to pay the balance of unused vacation days to employees in cash when they leave or retire. Though the University will pay for fewer vacation, personal and sick days, the short-term disability plan is expensive enough to offset some of those savings, Peel said.

The University reduced paid time off partly in response to the extra days off afforded by the short-term disability package, Peel said. Currently, staff who fall ill and cannot work must use up their vacation and sick days, a heavy burden for employees who are new or who have had multiple disabilities, he said.

“The change to add short term disability coverage, while still having paid time off at the top of the peer group, strengthens our comparative superiority,” he added.

But whereas managerial and professional staff currently receive 24 vacation days and four personal days a year, on July 1, these days will be combined into a single paid-time-off benefit of 24 days per year. Sick days will be halved from 12 days a year to six.

And in a move that represents major savings, the University staff will be able to carry over fewer vacation days from year to year, and the bonus vacation day program — under which the University granted longtime staff additional vacation days every five years — will be phased out starting this summer.

Between the reduction in vacation days and the added benefit of the short term disability plan, Yale will ultimately save “a few million” dollars on these adjustments, said University President Richard Levin, who announced the benefits adjustments in an e-mail to all faculty and staff with Provost Peter Salovey last Wednesday. About half of Yale’s spending every year goes toward personnel costs, including salary and benefits, Salovey said in December.

Staff can carry over up to 64 vacation days that they have accumulated from past years into the new fiscal year, which begins July 1, based on how long they have worked for Yale. But beginning July 1, 2011, they will only be able to carry over a maximum of 15 vacation days or the days they did not use during 2010-’11 — whichever is greater. For example, a staff member who has accumulated 27 days will keep up to 15, or the number of days not taken by July 1, for the 2011 fiscal year, which could be as many as 27 if he or she never vacationed.

Previously, staff could keep as many as 44 unused vacation days after the end of each year. Those who had worked for Yale for at least 10 years also received an additional bonus of five days per five years of service, which was granted once every five years, though these extra days were capped at 20, giving some staff a maximum of 64 days they could carry over each year.

“You’re giving up a little opportunity to take paid time off to get more when you need it,” Salovey said in an interview last week.

But now longtime managerial and professional staff will be losing their bonus days. Those who have already worked at Yale for ten years or more by July 1 will receive a final, one-time grant of bonus time on their next five-year anniversary of Yale service. If they have completed fewer than the five years needed to receive another five days, they will receive a fraction of the bonus. For example, an employee who has worked for 12.5 years will receive 2.5 bonus days during his or her 15th year of work.

While all the changes for managerial and professional staff take effect July 1, clerical, technical, service and maintenance staff who belong to Yale unions Locals 34 and 35 switched over to a new pay structure and revised benefits packages starting last month as a result of the new union contracts negotiated in April.