Philippine President Ferdinand Marcos Jr ordered law enforcement agencies to investigate and to determine measures to be taken to prevent violence in schools.
"Our schools are where we entrust our children to learn, to grow and to dream about the lives ahead of them. They must also be among the safest places in our country," Marcos said in a statement.
The shooting took place on Tuesday at a school attached to the privately run Ateneo de Zamboanga University in the city of Zamboanga, where the gunman brought a pistol and a rifle onto the school campus and fired at students inside the classroom, according to a preliminary police report.
Video aired by GMA News, with images blurred, showed chaotic scenes inside a classroom with students ducking for cover as several gunshots rang out.
The victim was a male grade 10 student, police said.
The gunman, a grade 9 student, killed himself, police said.
Two others were wounded.
The shooting followed an attack in June at a public high school in Tacloban City in the central Philippines in which at least three students were killed and about 20 others injured when two of their schoolmates opened fire on campus.
School shootings are rare in the Philippines, which has relatively strict gun ownership regulations, including background checks and psychological evaluation requirements, although illegal firearms remain in circulation.
News channel ANC showed footage of students and parents gathering outside the school gates with some armed police and soldiers present.
Crime scene investigators were seen arriving at the school.
The school is a five-storey building on an eight-hectare site that houses the university's grade school and junior high school students, according to its website.
The incident came less than 10 days after a high-profile incident in Thailand, where a student went on a shooting rampage at a school on the outskirts of the capital Bangkok.
