The bus operated by the Rural Transit company was travelling through the town of Maramag in the strife-torn island of Mindanao when the bomb went off, said spokesman Major Christian Uy.
The blast also injured 17 people.
The explosion was the latest in a series of attacks on the bus company.
Last month a bomb exploded aboard a Rural Transit bus in Mindanao, leaving four people wounded.
Ten people were killed when a bomb exploded aboard a bus operated by the same company on Mindanao in 2010.
Armed groups have proliferated in the southern Philippines since Muslim guerrillas began fighting in the 1970s to set up an Islamic state in that part of the largely Christian Philippines.
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