Demonstrators had overstayed their welcome and were disrupting students' education, Ms Allan said on Tuesday.
"We have reached a point where many Victorians are frustrated, are fed up with some of the reckless behaviour we've seen. I know I certainly am," she told reporters.
Jacinta Allan says many Victorians are fed up with some of the reckless behaviour on display. (Joel Carrett/AAP PHOTOS)
Ms Allan defended the right to peaceful protest but drew the line at violence from some.
"What we need to see is this reckless behaviour come to an end. Let those students who want to get back to learning, get back to learning," she said.
The premier's call comes as a group of Israel supporters crashed the stage of a pro-Palestine protest at Monash University's Clayton campus on Tuesday afternoon.
Four men holding Israel's flag wove through a crowd of about 50 students before positioning themselves on steps between speakers.
The action prompted pro-Palestine rally organisers to hold up keffiyehs in an attempt to block the flags from being visible.
Organisers said they recognised the interrupters from the university's encampment last week.
"These students are people we recognise," organiser Connor Knight told AAP.
"But we're not going to be intimidated by people holding flags."
Mr Knight is one of nine students facing suspension or expulsion for protesting at the campus.
He claimed the Israel supporters had not been threatened with action from Monash.
Police say no matter what decision is made about ongoing protests, they are in a no-win situation. (Rachael Ward/AAP PHOTOS)
Protesters said the Monash camp was "forcefully dismantled" on Friday, but the university said organisers had planned to pack up.
At the University of Melbourne students have occupied its Arts West building for a week.
Vice-chancellor Duncan Maskell said their occupation had led to the cancellation or rescheduling of more than 600 classes, disrupting more than 16,800 students.
"The university remains concerned and disappointed to see the refusal to leave the Arts West building on our Parkville campus," he said.
Professor Maskell told protesters on Monday the demonstration had become "increasingly disruptive and unsafe" and directed them to vacate the building.
Students and staff contravening the order were threatened with academic sanctions, including expulsion and may be referred to police for trespassing.
Police can only get involved when the university revokes someone's right to be on campus.
Officers have been involved in negotiations to end the sit-ins peacefully but would be forced to move in if that is unsuccessful, the police association said.
"The only losers out of that will be police because no matter what decision they take, they are going to have made the wrong one," union secretary Wayne Gatt told 3AW.
"If they use force, they'll have been said to have used too much. If they don't, they'll have been said to have stood back and watched too long.
"It's a no-win situation we can all see coming for coppers."
The University of Sydney has stopped short of ordering protesters to disband. (Dean Lewins/AAP PHOTOS)
La Trobe University has started misconduct proceedings against students who have failed to comply with an order to move on.
Organisers of a pro-Israel camp at the University of Queensland voluntarily disbanded on Saturday after the university asked for all camps to be removed but a pro-Palestine camp remains.
Police on Monday charged two 53-year-old men with high-risk activity after officers responding to calls of "political disturbance" found the pair on a university building roof.
University of Sydney vice-chancellor Mark Scott has apologised to students and staff who felt unsafe around the encampments there but stopped short of ordering them to disband to avoid escalating violence.
