Anthony Towey, head of the School of Theology, Philosophy and History at St Mary's University College, Twickenham, was suspended last week "pending investigations into a very serious disciplinary matter", the college has confirmed.
The action follows protests over plans to merge Dr Towey's department with the School of Communication, Culture and Creative Arts.
Academics at St Mary's, which hopes to become Britain's first Catholic university by 2013, fear the lack of a dedicated theology department may harm teaching and research as well as undermine the college's commitment to its Catholic mission.
Students told Times Higher Education that Dr Towey was interrupted while giving a Christology lecture on 17 September and escorted off the premises of the institution by a member of security.
His suspension comes after he sent an email to staff and students informing them about the proposed merger, saying he was "completely in the dark" about how it might affect students.
The email, seen by THE, criticises the "sudden decision" to merge the schools which he says "runs contrary to St Mary's procedures".
Dr Towey also mentions the "overwhelming and reasoned opposition to the proposal across some 60 academic and administrative staff" members and suggests students could complain to their union or the college's chair of governors.
"It is a tremendous sadness that this sense of community is being dismantled," he adds.
Dr Towey has distributed a document making detailed criticisms of the merger plans, which were put forward by the college's principal Philip Esler, a Bible scholar and former chief executive of the Arts and Humanities Research Council.
Lance Pettitt, head of the School of Communication, Culture and Creative Arts, has also said "the proposal to merge is ill-conceived, poorly researched and presents no coherent business case" in a draft response to the proposals.
However, St Mary's believes the merger will not only save money but will improve interdisciplinary research in religious studies.
A spokesman added that Dr Towey had been suspended following "a grave breach of his professional duties" and that his teaching programmes would be fully covered.