Students targeted Julie Bishop during an appearance at the University of Technology Sydney on Friday, while her fellow cabinet ministers faced more protesters interstate.
Police were also in attendance when protests spilled over to the University of Sydney campus, where students gathered with placards and banners.
Measures set out in Treasurer Joe Hockey’s federal budget on Tuesday mean universities and other higher education providers will be able to set their own tuition fees for courses from January 2016.
Students will fork out more when the government changes the rate at which they pay back their student loans.
Video obtained by SBS World News shows students chanting at Ms Bishop as she prepares to address an audience at the opening of the Australia-China Relations Institute at UTS.
A number of students chanted before being removed amid shouts of “shame on you”.
Another student heckled the Foreign Affairs Minister, saying that the government “don’t give a s—t about ordinary students”.
“Your attempts to attack university students are going to leave working class… students in poverty,” she said.
Protests were continued at the University of Sydney, where Student Representatives’ Council Education Officer Eleanor Morley said around 100 students gathered.
“We think Liberal politicians have no place in our university campuses,” she said.
Protester Brigitte Garozzo, a member of the Sydney University Education Action Group, told SBS the demonstration was to send a message to the government.
"Students at universities around the country are really unhappy about cuts to education that have been put through in the budget," she said.
Video uploaded to YouTube shows the Foreign Minister being jostled by university students.
But Ms Garozzo said the protest was non-violent.
"We will stand our ground and push back but we won’t throw punches and we won’t kick and we won’t hurt people," she said.
Brigitte Garozzo, who shot the footage below, speaks to SBS:
Ms Morley said protesters had also targeted Education Minister, who was speaking at Adelaide University, and Treasurer Joe Hockey who was addressing LNP members in Brisbane.
The protests come ahead of major action across the weekend and Wednesday, when education rallies will be held in every major city across Australia.