Violence, which included bullying and the continued use of corporal punishment in schools despite it being outlawed, was detracting from the Basic Education Department's core business of teaching and learning, MPs heard on Thursday.
Briefing Parliament's portoflio committee on basic education on school safety, department director-general Mathanzima Mweli said: "If we pay more attention on these issues, we don't have time to push issues of quality and efficiency in schools.
"This problem is bigger than us. It requires everyody. We can't run away from it unfortunately. It affects the space from where we are operating."
Mweli said many of the incidents of school violence was a spill over from violence in communities.
Referring to the shooting of a teacher in full view of pupils in Bushbuckridge, Mpumalanga, in August, he said it was related to family violence which made its way onto school grounds.
Gang violence in the Western Cape was also concerning as schools were not immune to this phenomenon.
"I've come across pictures of bodies lying all over the school grounds in the Western Cape here where learners have to walk over or across those bodies to go over to the classroom," said Mweli.
The department's collaboration with the SAPS was bearing fruit, but more needed to be done.
The committee heard that 23 064 out of South Africa's 24 844 public schools had been linked to local police stations to improve response times to incidents.
On corporal punishment, which has reared its ugly head via social media videos showing teachers beating pupils, he said teachers were being trained on alternate discipline, but he conceded this had not had much of an impact.
"It's very difficult for adults to unlearn behaviours inculcated over years," said Mweli.
"They were trained to teach badly by the apartheid government and over 80 percent of those people are still in the system and you are expected to improve results with them."
Mweli said several government departments, including social development, needed to become more involved in the fight against school violence.