FORT KENT — The University of Maine System board of trustees voted unanimously and without discussion Monday to cut three academic programs at the University of Southern Maine.

Also Monday, USM interim President David Flanagan told trustees that he will be proposing additional staffing and program cuts in January to help close a budget deficit for next year. The deficit has grown to $16 million because of lower-than-expected USM enrollment, which was down 5.3 percent as of Sept. 15, Flanagan said. That follows a drop of about 14 percent over the previous five years.

The trustees also voted to ask the Legislature to increase state funding by 3.4 percent to help close next year’s gap.

The trustees’ decision to cut three academic programs came after months of debate and after faculty leaders made a final public appeal to spare the American and New England studies graduate program, the geosciences major, and the arts and humanities major at Lewiston-Auburn College, which is part of USM.

“These program eliminations are a disaster, I believe, for the university,” said Paul Johnson, an associate professor with USM’s School of Social Work. Other speakers argued that the programs make money, help the local economy and provide general education courses for students in other majors.

“I’m not surprised, but I’m very disappointed,” USM Faculty Senate President Jerry Lasala said after the vote, which was one of several items on a trustees “consent agenda.”

The director of the systemwide faculty union said the group will likely challenge the trustees’ decision in arbitration.

“It’s definitely not over,” said Stephanie von Glinsky, director of the Associated Faculties of the University of Maine. The union argues that the proper procedures were not followed in ending the programs.

Trustees Chairman Samuel Collins defended the board, saying it was working with “great deliberation” to balance the budget across the university system.

“Those are very difficult decisions,” Collins said. “But we do have to face the dire circumstances that are before us, and the fact that the structural gap is not going away.”

The latest systemwide budget of $529 million, approved in May, cut 157 positions and required $11.4 million in emergency funds to close a $36 million deficit. Without changes, the deficit would grow to $69 million by 2019, officials project.

USM officials needed $7 million in emergency one-time system funds to help close a $14 million gap in the school’s $134 million budget for the fiscal year that began July 1.

No new students will be allowed to enroll in the programs eliminated Monday. Current students in those programs will still be able to get their degrees at USM, with the programs and their seven faculty members being phased out as demand decreases.

As of June 11, there were 57 students majoring in American and New England Studies, 61 students majoring in arts and humanities in Lewiston, and 47 students majoring in geosciences, officials said. USM had a total of 8,124 students at its Portland, Gorham and Lewiston campuses as of Sept. 15.

The cuts, first proposed in the spring, led to student and faculty protests, including a march through downtown Portland. In recent weeks, student leaders have criticized the trustees for holding the vote on the programs in Fort Kent, so far from the USM campus. The board rotates meeting locations and had scheduled the meeting in Fort Kent months ago.

No USM students spoke at the trustees meeting Monday.

Flanagan already had warned trustees that USM faced additional cuts to close an anticipated $15 million deficit for the fiscal year beginning next July 1. He said Monday the deficit is now expected to be $16 million because of the lower-than-expected enrollment this fall.

He said he would lay out his strategy to close that $16 million gap by January, when he presents the school’s budget to the trustees.

Flanagan said Monday there would be more staffing and program cuts, along with new marketing and recruitment efforts.

In addition, he said, he will ask the trustees for approval to offer “more flexible” tuitions, as some other University of Maine campuses do. Flanagan said he would initially target tuition rates for graduate students from out of state, noting that USM had very few of those students and a more attractive tuition rate could help recruitment.

Trustees also talked Monday about the need for additional consolidation in other parts of the university system, as well as the need for more revenue systemwide.

Several trustees said they supported a proposed reorganization that would result in closing the system’s central office in Bangor and moving those jobs to campuses throughout the state.

It is one of several proposals being considered for streamlining the administrative functions of the system, said Rebecca Wyke, vice chancellor for finance and administration. Wyke did not have any specifics on the time line or financial impact of such a move. A final proposal will be brought before the trustees at their November meeting.

The system will ask the state to increase funding by 3.4 percent, from $176.2 million to $182.2 million, for the fiscal year ending June 2016. In the second year of the state’s biennial budget – ending in June 2017 – they will ask for an increase of 3.8 percent, to $189.1 million.

Currently, state funding brings in 34 percent of the system’s operating budget, and tuition brings in 42 percent. Over the past three decades, state funding has provided as much as 72.5 percent of the system’s operating budget, and tuition has paid for as little as 22.9 percent, trustees Chairman Collins noted Monday.

In inflation-adjusted figures, Maine’s education appropriation per full-time-equivalent student has dropped 15 percent over the past five years, from $7,027 to $5,978, according to a national survey and analysis by the State Higher Education Executive Officer Association.

Systemwide, total enrollment is down 3.2 percent. There were 29,253 students on Sept. 15, down from 30,215 students at the same time last year.

Despite the overall downward trend, nonresident enrollment, which brings in more revenue, is up 7.4 percent systemwide, from 4,235 students last year to 4,547 this fall. All campuses have fewer students this fall except Fort Kent, where enrollment increased 11.2 percent, to 1,342 students.