The child was lost as his family joined some 39 other families who fled waist-deep waters on 11 villages on the town of Sultan Mastura before dawn, said the town Mayor Armando Mastura.
Several "millions of pesos" worth of rice and corn crops were destroyed, he added. A dollar is worth around 50 pesos.
Six other villages were flooded in the adjacent town of Sultan Kudarat, forcing some 20 other families to flee to higher ground, local officials said.
Heavy rain has soaked the Cotabato river basin of Mindanao over the past two weeks, residents said.