Benigno Aquino says police discovered a plan by the terror group Abu Sayyaf to kidnap the world-famous fighter and plant bombs in the Filipino capital Manila.
The group was hoping to get funding from Islamic State by carrying out the attacks, the president revealed.
Manny Pacquiao has often spoken about his devout Christian faith and how it helped him change his life: "I knew I could do whatever I wanted. But I changed when I heard the voice of God, and I can testify that there is a God.
"I saw two angels, white, long, big wings. I saw Paradise. God showed me about the end of time. This all happened within the last three years. That's how I changed my life."
The 37-year-old, who is currently running for a seat in the Philippine's Senate, said he was "alarmed" when told about the plot.
"We asked for security, protection for my kids, my family to make sure they are safe, especially as I'm not there right now," he said.
The boxer has since been seen with a visible increase in security staff around him.
"I doubt [the threat] but I'm not ignoring it," he told reporters.
"I live my life like every day is the last so I have no fear. God is with me."