Police then fired rubber bullets on the crowd and four demonstrators were hurt, the AFP reporter said, while another four were injured in clashes with officers.
The eight were taken to the local hospital but a doctor there indicated none of their injuries were serious.
Rally organisers, the youth secessionist West Papua National Committee (KNPB), also said four people were shot at the protest and taken to hospital.
"They punched me twice in the face and tried to strangle me. They hit other journalists and I saw at least two people get shot," Pogau said.
Manokwari police chief Agustinus Supriyanto declined to comment on the violence and would only say that the incident was being evaluated.
Police had rejected the students' request to demonstrate outside the university and ordered the demonstration be shut down.
The demonstration was one of several in Papua on Tuesday which were organised by the KNPB ahead of a meeting later in the day in London of international lawyers who are backing a Papuan independence referendum.
International watchdog Human Rights Watch (HRW) condemned the police action, saying the students had a right to protest.
"Police should stop the excessive use of violence in Papua. It should investigate officers who ordered the violence," Jakarta-based HRW researcher Andreas Harsono said.
The protests were the first major pro-independence rallies since Indonesian police shot dead KNPB's deputy chairman Mako Tabuni in June, which sparked a wave of anger that saw cars and homes set ablaze.
Papua - a vast, mineral-rich region in the east of Indonesia that shares an island with Papua New Guinea - has a mostly Melanesian population, ethnically different from most Indonesians.
Jakarta annexed the former Dutch colony in 1969 and has since faced a low-level insurgency