The students along with 60 other fellow activists had refused to disperse after repeated warnings were issued by Tanjung Malim OCPD Othman Nayan.
The group instead moved to the locked university gate and rattled it, demanding it be opened for them to enter the campus.
Subsequently, the police, numbering at about 30, moved in and forcibly grabbed the protest leaders, many of whom resisted.
Among them was Kumpulan Aktivis Independen Mahasiswa (Kami) president Haziq Abdullah Abdul Aziz, who was cornered by three police officers but with his muscular build, he managed to throw them off.
Five other police officers joined the fracas and they finally pinned the student leader down to the ground.
Haziq Abdullah later lost consciousness as the police were about to carry him away, but journalists at the scene were suddenly distracted by a loud bang.
The noise came from a nearby clinic where the students had broken the door in the attempt to seek medical attention for another student leader, Gerakan Menuntut Kebebasan Akademik (Bebas) president Muhammad Safwan Anang, who had went into a fit.
However, Muhammad Safwan (right) was unable to get treatment there and the students soon left the clinic. Muhammad Safwan was immediately put into a vehicle and driven away, presumably to a hospital.
It was unclear if a doctor was present at the 24-hour clinic but a medical staff told Malaysiakini that they were unable to treat such condition.
A witness who helped carry Muhammad Safwan into the vehicle said the student leader had grabbed his chest and he saw that the student leader's mouth was bleeding.
"Everyone were distracted by the arrest (of the other students). When I looked behind me, I saw three police officers trying to subdue Safwan. Then he went limp and started to shake. There was blood on his mouth," he said.
Arrests made at 2.40am
When police confronted them, they dispersed and regrouped at the main gate of the university at 2am, chanting "Bebas, bebas! Bebas Mahasiswa" (Freedom! Freedom! Free the Students).
The students activists were there to show solidarity to Legasi Mahasiswa Progresif (LMP) Adam Adli Abdul Halim, who was also present at the demonstration.
Adam Adli (left), also a UPSI student, faces disciplinary action from the university authorities for lowering a flag of Prime Minister Najib Abdul Razak at the Umno headquarters in Kuala Lumpur during a march last month.
When police arrived at UPSI's main gate, the students lied down on the road and refused to budge.
They later stood nose-to-nose with the Light Strike Force officers, chanting slogans and unfurling a 30-metre long banner reading, "Bebaskan Mahasiswa!".
The clash occurred minutes later - at about 2.40am - when the group moved closer to the UPSI gate.
By 3pm, most of the male students were either arrested or had accompanied Muhammad Safwan to the hospital, leaving behind female student protesters whom the police did not act against.
The remnants of the student group subsequently left the area as police cordoned off the area.
PSM member also nabbed outside police station
The university sit-in today was jointly organised by two student groups - the Solidariti Mahasiswa Malaysia (SMM) and Bebas.
SMM in a Twitter posting confirmed that Muhammad Safwan had been sent to Tanjung Malim hospital. He was later transferred to Slim River Hospital.
At least two protesters had suffered injury at the scene, but more photographs of injuries have surfaced on Twitter.
Another arrest was made at about 4am when Mandeep Singh, a Parti Sosialis member, chanted "Bebaskan Mahasiswa" outside the Tanjung Malim police station where the arrested activists were held.
According to PSM, Mandeep reported from inside the police station through short text message that a total of 17 students had their statement recorded there.
PKR Youth deputy information chief Rozan Asen Mat Rasip along with pro-opposition groups - Jingga 13 and Asalkan Bukan Umno (ABU) - were at the police station to offer assistance to the detained students.
Rozan said he was informed that Muhammad Safwan had suffered a broken rib and he was believed to be in a serious condition.