One young man who was picked up by the police, beaten and then released after a month and a half in detention said he had moved to his grandmother’s house in a different district of Manila to hide.

When he returned to visit his neighborhood, one of his friends told him that vigilante gangs were looking for him. It was a warning he took seriously. One of his friends had already been killed.

“I was afraid,” he said, adding that he has had trouble sleeping at night. “I thought they were going to kill me.”

His mother worried that if he stayed in Manila, he would be shot, so she made him move again, to a rural village of bamboo huts, dirt roads and banana trees in the northern Philippines. He texts with his friends, but tells them that he is in a different part of the country, just to be safe.

His mother said she had voted for Mr. Duterte, but now wishes she could take her vote back.

The clergy providing sanctuary, part of a coalition called Rise Up, operate in secret, fearing the church’s protection will not be enough to keep vigilantes from coming after them.

“The most vulnerable are always an easy target, even if they are under our sanctuary,” said Jun Santiago, a lay brother of the Congregation of the Most Holy Redeemer and a member of Rise Up. “We don’t know who the killers are.”