Security forces were placed on full alert in the southern Philippine region of Mindanao following a deadly suicide bomb blast in Basilan province that killed 10 people.
Ucanews.com reported the cardinal's questions and plea came a day before the Philippine Catholic bishops issued a statement condemning the killings across the country.
The Philippine immigration bureau on Thursday ordered the deportation of an Australian nun who has angered the president by joining anti-government rallies, but her lawyers called the move "persecution" and said they would appeal.
Outspoken Philippine President Rodrigo Duterte is to curb his tirades against the Catholic Church after agreeing to a moratorium on statements deriding priests and bishops.
Philippine Catholic bishops on Monday called for fasting and prayers after President Rodrigo Duterte called God "stupid" and questioned God's existence in profane remarks that set the foul-mouthed leader on a collision course with Asia's largest Catholic church.