The faculty senate, meanwhile, took a vote of no confidence Tuesday against Louis J. Mayer, vice president of financial affairs, and John Smithson, senior vice president, a faculty member confirmed.
Robert Moore, faculty senate president, did not return calls for comment Tuesday.
University spokeswoman Harriet Goodheart said the university had not been told of the vote and declined comment. Goodheart confirmed that provost Brice Wachterhauser will step down June 1.
In explaining the shortfall, Goodheart said the university aims to operate with a 3 percent surplus in its $230 million budget and is $8.7 million short. To help make up the difference, the university cut operating budgets across campus by 4.2 percent earlier this year, she said. It also plans to enroll 1,500 freshmen next fall, up from 1,275 in fall 2013.
That announcement has caused some students to worry about larger class sizes and express concern that the university might lower its standards to bring in additional tuition revenue. President C. Kevin Gillespie said that would not be the case.
"I am extremely dismayed that a freshman enrollment target has become the flash point for so much anger on the campus," he said in a statement. "We will not compromise academic quality by admitting students who cannot succeed at St. Joseph's, even if that means falling short of enrollment targets or capping the admit rate."
In 2012, the most recent year for which public tax documents are available, St. Joseph's ran a $4.4 million deficit.
University officials said the tax document is not the best measure of financial stability.
"During a challenging period in higher education, St. Joseph's University has maintained an extremely strong market position with 'A' financial ratings," Gillespie said.