Archbishop Socrates Villegas of Lingayen-Dagupan said in a letter to members of the Church that "murders continue without relent".
He added: "God's justice be upon those who kill the Lord's anointed ones. There is a special place in hell for killers. There is a worse place for those who kill priests."
Two gunmen killed a priest as he prepared to celebrate Mass at the altar of a chapel in the north of the country on Sunday.
The killing is the latest deadly attack on priests in Asia's largest predominantly Catholic nation. The two men shot the Rev Richmond Nilo with pistols in the chapel in Zaragoza town in Nueva Ecija province.
Fr Tito Paez was killed in December 2017 and Fr Mark Anthony Ventura was killed in April this year.
Archbishop Socrates called for the Church to observe "day of reparation" on 18th June.
He encouraged Christians to "stand up for the Lord and courageously correct error and sin" and "work actively for social and political changes grounded in Catholic moral teachings and Christian social ethics".
18th June will also be a day of fasting and abstinence for the priests and other leaders in the Church.
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