A total of 450 kilos of ammonium nitrate, a key ingredient in making improvised bombs, was recovered on a ferry docked in a port in Zamboanga City, 875 kilometres south of Manila.
The chemicals were placed in nine sacks, which the crew said were declared by its unidentified owner as containing dried fish, according to the police report.
Six crewmen of the ferry, including its captain, were detained at a police station in Zamboanga City for questioning.
The discovery came as the police and military were on high alert in key cities in the southern region of Mindanao amid warnings of possible terrorist attacks.