Scott Morrison rushed from protesters after red paint thrown on his car
Videos show dozens of protesters chanting "free the refugees" outside the building, where Mr Morrison was visiting a vaccine lab, and asking to speak with him.
A Queensland Police Service spokesperson said the protest action began outside the university, during which Mr Morrison's car was damaged, and he was later escorted by officers from the building and into a police vehicle.
Asked about the protesters at a media event later in the day, Mr Morrison said their actions were "very disappointing".
Refugee rights activists in Brisbane have this year repeatedly protested outside the Kangaroo Point Central Hotel, where some 120 asylum seekers are being detained.
They have long criticised Mr Morrison and the coalition government for its hardline immigration and border polices.
In 2018 Mr Morrison attracted international attention when it was revealed he had a trophy in the shape of a migrant boat with the caption "I Stopped These" in his office, in reference to his overseeing of the government’s Operation Sovereign Borders policy during his time as immigration minister.
A few months later, he told an event organised by suicide prevention service Lifeline that he has cried “on his knees” over the plight of young asylum seekers held in Australian offshore processing centres, saying border security was a “moral burden” and the issues were not “easy”.
Thirteen people have died while in Australia's offshore processing system since it resumed under the Gillard Labor government in 2012, according to the Refugee Council of Australia.