Columbia University has threatened student protesters with "clear consequences" after protesters occupied a building in an escalating standoff. Students defied a 2 p.m. deadline to disperse Monday.

Students occupying the building face expulsion, the university warned.

"We made it very clear yesterday that the work of the University cannot be endlessly interrupted by protesters who violate the rules. Continuing to do so will be met with clear consequences. Protesters have chosen to escalate to an untenable situation—vandalizing property, breaking doors and windows, and blockading entrances—and we are following through with the consequences we outlined yesterday," Columbia said in a statement.

Students who did not commit to the terms Columbia's proposed agreement to vacate the encampment by 2 p.m. Monday have been suspended.

"Those students will be restricted from all academic and recreational spaces and may only access their individual residence. Seniors will be ineligible to graduate," Columbia said.

"This is about responding to the actions of the protesters, not their cause," Columbia said.

Columbia University said it has limited access to its Morningside campus except to students residing in seven residential buildings, labs and employees who provide essential services.

The school has also limited access into and out of the building to one gate, closing all other campus entry points.

The restrictions will remain in place "until circumstances allow otherwise," Columbia said.

New York Police Department officers said they would not enter the property unless Columbia requests it, or there is an imminent threat.

Virginia Tech said it has cleared an encampment on campus and arrested 82 protesters for trespassing, after refusing to comply with university policies.

"Virginia Tech strongly supports free speech, even when the content of that speech may be disagreeable to some. However, those rights do not extend beyond the point where they interfere with the rights of others, violate our policies, the Code of Virginia, or federal laws and/or create a threat to safety for others," Virginia Tech President Tim Sands said in a statement.

Meanwhile, Virginia Tech Muslim Student Association said in a letter the 91 students faculty and staff were arrested for peacefully protesting.

"As we reach the end of the semester, 7 months after Oct. 7, we are finding our voices still unheard. We are waiting for your support of us and Palestine," the Virginia Tech MSA said in a statement.

-ABC News' Nadine El-Bawab and Kerem Inal

California State Polytechnic University, Humboldt said it has cleared two campus buildings that had been occupied by protesters for over a week and arrested 25 people.

"Those arrested faced a range of different charges depending on individual circumstances including unlawful assembly, vandalism, conspiracy, assault of police officers, and others. In addition, students could face discipline for conduct violations while any University employees arrested could face disciplinary action," Cal Poly said in a statement.

The university called the occupation of the two buildings "criminal activity" and said there were "serious concerns it would spread even further on campus."

"This morning’s enforcement action was determined to be necessary to restore order and to address the lawlessness and dangerous conditions that had developed. What was occurring was not free expression or a protest," the university said in a statement.

The campus will remain closed until May 10.

Columbia University has distributed a letter to members of the encampment on campus telling them to gather their belongings and leave the area by 2 p.m., saying if they identify themselves and sign a form "to abide by all University policies through June 30, 2025, or the date of the conferral of your degree, whichever is earlier, you will be eligible to complete the semester in good standing."

The school said it has "already identified many students in the encampment" and "if you do not identify yourself upon leaving and sign the form now, you will not be eligible to sign and complete the semester in good standing." The school warned it could take action up to suspension or expulsion if they do not leave the encampment.

The school reiterated that negotiations with protesters had broken down and said the protests are a "disruption" to those taking final exams and preparing for graduation.

"As you are probably aware, the dialogue between the University and student leaders of the encampment is, regrettably, at an impasse," the letter states. "The current unauthorized encampment and disruption on Columbia University’s campus is creating an unwelcoming environment for members of our community. External actors have also contributed to this environment, especially around our gates, causing safety concerns – including for our neighbors."