Hundreds of students across the University of Melbourne, RMIT, Monash, Deakin and Latrobe universities have pitched tents and staged campus sit-ins since April.
Students have also set up camps at campuses in Brisbane and Sydney.
The groups have vowed not to move until their institutions cut ties with Israel and associated weapons manufacturers in protests mirroring others involving students around the world.
Some language used on campuses has been anti-Semitic and universities needed to be "safe spaces for all students, regardless of who they are", Foreign Minister Penny Wong said.
But she also acknowledged there was a right to peaceful protest.
"We must defend people's right to disagree respectfully," she told ABC Radio on Friday.
Broad statements branding protesters and chants as anti-Semitic needed to be avoided, Prime Minister Anthony Albanese said.
But "from the river to the sea" was not appropriate because it went against a two-state solution when used by either the Palestinian or Israeli side, he said.
Police say there is a strong likelihood of clashes between protest and counter protest groups. (Joel Carrett/AAP PHOTOS)
"Some of the reduction to simple slogans without any understanding of history is not appropriate," he told reporters in Canberra.
Victoria Police is warning universities that there is a strong likelihood of violence if student encampments are not disbanded and counter-protests are uncontrolled.
There was concern about the number of protesters who were not students "inflaming the situation", Deputy Commissioner Neil Paterson wrote to university chancellors on Thursday.
Police were being called daily to camps with complaints, he said.
"Police believe there is a strong likelihood of violence occurring between protest and counter-protest groups as well as other criminal offences occurring such as property damage if the encampments continue to grow in size," a Victoria Police spokeswoman said.
Students for Palestine organiser Madeline Curkovic said their protest was peaceful but alleged members of the pro-Palestine encampment had been attacked by pro-Israel supporters.
She said they planned to press charges.
Pro-Palestinian and pro-Israeli protesters faced off at the University of Melbourne on May 2. (Joel Carrett/AAP PHOTOS)
The Australasian Union of Jewish Students (AUJS) has been contacted for comment.
The union said students had met with Education Minister Jason Clare "to address the troubling escalation of anti-Semitism on university campuses".
"We emphasised to the minister that we support peaceful protests on campus, which is a fundamental right," it said in a statement on Friday.
"However, we demanded clear red lines to address rising anti-Semitism."
Tensions escalated at the University of Melbourne's encampment when dozens of Israeli supporters arrived on May 2.
AUJS president Noah Loven told supporters his group stood in opposition to the encampment.
Several hundred pro-Israel supporters gathered earlier at University Square, led by Jewish students who said they felt unsafe on campus.
8°C