La Trobe University has started misconduct proceedings against students, while the University of Melbourne ordered protesters to remove belongings from a building and move on.
Monday marks the sixth day students have occupied the Arts West building at the university's Parkville campus.
More than 15,000 students across 474 classes have been affected and alternative arrangements were being made on Monday and Tuesday, the university said.
The building was closed on Friday following a safety inspection which found damage and obstructions to emergency exits, fire panel access and firefighting equipment.
Pro-Palestine encampments remain on the grounds of a number of Australian university campuses. (Con Chronis/AAP PHOTOS)
Vice-chancellor Duncan Maskell on Monday issued a notice to protesters saying the demonstration had become "increasingly disruptive and unsafe".
"Camping is not allowed on university premises. Occupation of buildings is not permitted," he said.
"The university directs all persons occupying the Arts West building to leave the university's grounds and to remove all personal property from the building."
Students and staff contravening the order have been threatened with academic sanctions including expulsion and may be referred to police for trespassing.
Victoria Police said the university had not asked officers to intervene.
"If we are asked to do anything, (we want to make sure) any response is proportionate ... and if we do go in, there'll be negotiations with those protesters before any action takes place," Acting Assistant Commissioner Mark Galliot told ABC Radio on Monday.
"At this stage, we do not want to act and the university doesn't want to act because they want to seek a peaceful resolution to what's occurring."
La Trobe University in Bundoora cited health and safety as the motivation behind why it called for protesters to disband their camp.
The university will start misconduct proceedings against students for failing to comply with an earlier order to move on.
Earlier on Monday, about 30 students demonstrated in front of almost two dozen tents chanting "from the river to the sea, Palestine will be free" and other slogans.
They have demanded the university not evict them, no academic discipline be taken against student protesters and all ties be cut with engineering conglomerate Honeywell and Israel.
Organiser Maeve Russack said students would continue protesting regardless of what happens to the encampment.
"Our position on this is that we are a peaceful protest. The university has recognised this," Ms Russack told AAP.
Student demonstrators want universities to refrain from taking academic action against them. (Joel Carrett/AAP PHOTOS)
Deakin University students will close their camp on Thursday, but have vowed to be back at the start of the next semester.
University of Sydney vice-chancellor Mark Scott has apologised to students and staff who feel unsafe on campus as demonstrators promised to continue their encampment, not ruling out moving inside like students in Melbourne.
But Mr Scott has not ordered the encampment to disband to avoid "going down the United States route" where violence has broken out after universities and police tried to clear encampments.
"It embodies debate, discussion, free speech and protests that's always been part of university life," he told 2GB radio on Monday.
"If there's criminal action that takes place at the university, we will call the police."
Monash University protesters claimed their camp was "forcefully dismantled" on Friday, but the university said organisers had told them of plans to pack up the encampment.
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.
Student protesters at the Australian National University in Canberra have been told to leave or the university could consider disciplinary action.
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