In April scores have died in a series of attacks and assassinations in Mexico, the Philippines and Nigeria. Catholics at prayer during Mass have been targeted in a number of attacks.
Immigration officials have accused the nun, who has worked in rural communities for 27 years, of being an "undesirable alien" for joining protest rallies and visiting political prisoners.
Manila Cardinal Luis Antonio Tagle washed the feet of a priest who had been held captive for months and the parents of a slain Filipino migrant worker.
Bishop Edwin de la Pena of Marawi assured Catholics in the region that other parishes not affected by the fighting will continue their ministries.