Human Rights Watch and politicians said Rodrigo Duterte's words could encourage the military to attack children and teachers.
Schools are supposed to be places of safety - where children can learn and be with their friends without feeling fear.
Almost 70 countries have signed up to the Safe Schools Declaration, which is a commitment to protect schools from being attacked or used for military purposes.
But the President of the Philippines has shocked human rights campaigners by threatening to bomb schools for indigenous Lumad children in the south of the country.
In a televised news conference, Rodrigo Duterte claimed schools were being run by Lumad insurgents to teach "subversion and communism".
He said: “Get out of there, I’m telling the Lumads now. I’ll have those bombed... I will use the armed forces, the Philippine air force.
"I’ll really have those bombed … because you are operating illegally and you are teaching the children to rebel against government.”
His words were condemned by human rights groups and politicians.
“By calling for an attack on schools Duterte is directing the military to commit war crimes,” said Carlos Conde of Human Rights Watch.
He urged the president to sign the Safe Schools Declaration, which has been backed by 67 countries. Conde added: “It’s clearer than ever that the Philippines should do likewise.”
Congresswoman Emmi de Jesus of the Gabriela Women’s party asked Duterte to withdraw the threat. She said government troops could use it as an excuse to attack indigenous schools and communities.
Datu Jomorito Goaynon, regional chairperson of the tribal group Kalumbay in Northern Mindanao, said the president's words could put the lives of students and teachers in danger.
He added: “It will only embolden the government agents to commit more violations against the Lumad people, especially now that we are under martial law."
Duterte recently called off peace talks with Maoist guerrillas who have been waging an insurgency for almost 50 years.