Organised by Otago Students for Justice in Palestine, the rally was calling on the University of Otago to suspend collaborations with Israeli universities and join the BDS (boycott, divestment and sanctions) movement against Israel.
A spokesperson for the group said the protest was planned as "peaceful direct action", in which they planned to "occupy" the clocktower.
"We were obstructed by Campus Watch, who physically blocked us from entering the building."
Two members of the group managed to enter the clocktower after being blocked, they said.
One person was detained by a Campus Watch staff member, and after an altercation a glass plane was smashed.
They thought it was "a gross overreaction considering what we were doing".
Once the glass smashed, the group of between 100 and 200 people stopped trying to enter the building and formed a line in front of the clocktower.
Protester Rosie Cruickshank said the group wanted the university to "make a stand about the genocide in Gaza" and support the BDS movement.
"We were staging a peaceful protest outside and we entered the clocktower — as many students have done before us — but we have been removed now and one person was arrested for wilful damage."
University of Otago vice-chancellor Grant Robertson said it was "important that students and staff are able to express their views and protest within the law".
"This protest crossed that line.
"This is against the kaupapa of our community and is not welcome."
Police were notified that damage had been sustained at the clocktower and it was locked down as a precaution, a spokeswoman said.
"One person has been arrested.
"They have been referred to Te Pae Oranga for alternative resolution," a police spokesman said.
