Police were called to the University of Aberdeen following a disturbance at a protest over pensions.
On Tuesday about 18 students occupied the senior management corridor at the administration building in Regent Walk.
The university said a member of staff was knocked to the ground when more students protested on Wednesday.
Students claimed a member of the protest called police after becoming concerned at the "heavy handed" response of university security staff.
The occupation is in solidarity with academics involved in the University College Union (UCU) pension dispute.
A University of Aberdeen spokesperson said: "Police were called to the University Office this afternoon by our staff following an incident whereby a group of protesters forced their way into the building, leaving staff shaken and distressed and resulting in one staff member being knocked to the ground and having their head trodden on.
"As frightened staff were forcibly pushed aside by the group they protected themselves as best they could but categorically deny inappropriately handling any individuals. We are extremely disappointed with this turn of events."
The university said it supported the students right to peaceful protest, and that the original group of protesters had been given food and blankets.
The spokesperson added: "A note granting the original group of demonstrators access to the building has been wrongly interpreted as a right for them and other students not involved in the original group to roam the building freely and come and go as they please.
"This was never intended to be the case as it would result in the University being unable to assure the safety of our staff or students."
The UCU said: "Onlookers outside the building - including University of Aberdeen students and staff - were extremely concerned about the safety of the students inside the building holding a peaceful protest.
"The instruction from management to place security guards and keep doors locked in an entrance corridor had caused a situation where students and staff were enclosed in a very small space and we were concerned for their safety.
"It seemed an unnecessary action during what the university themselves had called a peaceful protest, and to ensure the safety of students a UCU representative called the police."
On Tuesday, strikers turned down an agreement reached by university union leaders and employers to end the dispute.
It means the strike will continue - with threats to disrupt final exams and assessments in the summer term.
The action, now in its fourth week, has disrupted classes at more than 60 universities, including eight in Scotland.