Tuition will not be increased for the spring semester, which starts in January, but could go up next fall, Magee said.
Layoffs are not expected, he said, and sports teams will not have to reduce their trips.
"We don't want to decrease the services that we are providing to our students," including student athletes, Magee said.
Shepherd has faced similar situations in past years, and was once ordered to cut spending by 5 percent during the final quarter, said Magee, who has been at Shepherd since 1985, and in his present position since March 2001.
"This (cut) is earlier and smaller than some and larger than some," Magee said. "We have dealt with them before. That doesn't mean that they aren't difficult to deal with."
Wise's cuts, which are effective Jan. 1, will not apply to public education, corrections, Medicaid, the Children's Health Insurance Program, or the State Police.
During an afternoon press conference Tuesday in Charleston, W.Va., Wise proposed tripling the cigarette tax, erasing 2,097 vacant state positions and eliminating another 2,000 through retirements and resignations.
"To ease public employees, we do not anticipate layoffs for the balance of this fiscal year," Wise said. "However, the next fiscal year presents much greater challenges."
Some of those 2,097 job vacancies are state trooper positions, but Sgt. Deke Walker, stationed out of the State Police's Charles Town, W.Va., barrack, said he is optimistic.
"My understanding is that it's not going to affect us at all," he said. "I'm not sure how much more we could cut back."
Five years ago, 45 troopers were stationed among Berkeley, Jefferson and Morgan counties, he said. Today that number has dropped to 31, including two officers temporarily assigned to the area.
The Associated Press contributed to this story.