This weekend, faculty in the largest college at Emory University are expected to begin casting online ballots over whether President James Wagner is fit to lead the respected private school.

Many of those who teach in the College of Arts and Sciences have been angry since program cuts were announced in September. The cuts could threaten academic quality and hurt minority students since the affected graduate-degree programs produce a high number of minority degree holders, faculty said.

For some the disappointment in Wagner intensified after an essay he wrote that many thought appeared to glorify a compromise that classified slaves as less than whole people.

At the root of nearly all the frustration is a communication problem. Some feel Wagner has marginalized faculty and cut them out of important decisions about the institution’s future and direction.

Emory is among many colleges across the country facing communication battles as they grapple with a rapidly changing landscape forced by economic demands, new technologies with online learning and the desire to improve global outreach. Last month the largest college at New York University voted no confidence in its president, saying he failed to consult with them about ambitious plans to expand the colleges’s physical campus and global exposure.

“President Wagner is in a very challenging spot and it is very public, but every institution I know is grappling with these issues in one manifestation or another,” said Molly Broad, president of the American Council on Education, an influential umbrella group for higher education.

A president runs a college, but faculty have long had a say in everything from curriculum to program development, building usage, and overall policies and procedures.

However, as colleges have become more complex and need to quickly respond to the evolution of higher education, big decisions are being made without the full consultation of faculty, said Hunter Rawlings, president of the Association of American Universities. Emory is part of that group, whose members are leading public and private research universities.

“All of us value this shared decision-making, but we are all asking to what extent can it continue,” he said. “Universities need to define the areas in which faculty share in decision-making. I’m not saying these discussions will be easy.”

Emory is closing its educational studies division, its physical education department, its visual arts department and its journalism program. It’s also suspending admissions to the graduate programs in Spanish, economics and the Institute of Liberal Arts.

Savings from the changes will be re-invested into existing programs and growing areas, such as neurosciences, contemporary China studies and digital and new media studies, officials have said.

Since the cuts were announced many faculty have questioned whether Wagner understands what faculty do and the importance of liberal arts for Emory. Nearly 500 faculty work in the College of Arts and Sciences, while Emory has nearly 3,000 faculty in nine schools.

“There is a large gap between what we expect from him and how he relates to us,” philosophy professor Cynthia Willett said after a recent faculty meeting with Wagner. “There are serious questions about his leadership, and many of us feel that the way he conducts business is just not right.”

Robin Forman, dean of the College of Arts and Sciences, wrote a letter to faculty in defense of Wagner after they decided to move forward with a vote of no confidence. Forman wrote that Wagner is a strong supporter of liberal arts and said he has heard him advocate its importance to trustees.

Wagner declined requests for an interview for this article and has repeatedly declined to speak with the media since the uproar over his essay nearly two months ago. He has repeatedly apologized for the column and its use of the compromise, which counted slaves as three-fifths a person for determining representation in Congress.

If the faculty vote no confidence in Wagner it would send the message they are unhappy with his leadership. It won’t affect his employment status. That decision rests with the trustees, wh0 have stressed their support for him.

Regardless of the outcome, faculty and Wagner are partners who need to work together, said Stefan Lutz, an associate professor of chemistry and chairman of the faculty governance committee for Emory College.

“Faculty have a vested interest in the success of the college but it doesn’t always come across that administrators recognize that,” he said. “At the same time, running a 21st-century institute of higher education is not trivial, especially in trying economic times. We all need to compromise to find solutions to the problems the university faces.”