The shooting reportedly took place at a school attached to the university.
The deceased included two security guards. Authorities have not yet released the identities of those killed.
According to The Manila Times, the shooter was identified as a male fourth-year high school student whose father reportedly worked at the Zamboanga City Customs Office. The report said the student was carrying a Glock 9mm firearm and an M16-style rifle.
Ateneo de Zamboanga University said it was coordinating with authorities to establish the full details of the incident.
“As for other information, we are coordinating with authorities for the full report with full details to be provided as soon as possible,” the university said.
“The safety of our students is our top priority. We have already coordinated with parents and guardians to pick up their children and the university has ensured the safety of those remaining on campus,” it added.
The Philippines' Department of Education said it was “gravely concerned” about the shooting and expressed solidarity with the Ateneo de Zamboanga community during the difficult time, The Manila Times reported.
School shootings are relatively uncommon in the country mainly due to strict firearms regulations.
The latest incident occurred just days after a student went on a shooting rampage at a school on the outskirts of Thailand's capital, Bangkok.