Father Sebastiano D'Ambra has been highlighting his concerns to the Catholic charity Aid to the Church in Need.
He's been speaking about concerns of extremism after 14 people were killed during attacks on Christmas Day, which included a grenade being thrown at a chapel.
He said: "In some areas of Mindanao we are experiencing exactly the same thing as is happening in Iraq.
"It is difficult to establish for certain whether the violence was directed specifically against Christians, even though everything points to the fact that this was the case.
"Without doubt, our brothers and sisters in the faith are one of the targets of these fundamentalist groups."
It's claimed extremist group Bangsamoro Islamic Freedom Fighters, which has links to Islamic State, is behind a number of attacks on Christians on the island.
Father D'Ambra says the group is taking advantage of the uncertainty ahead of the 2016 government elections.