Rescuers lowered tubes to pump water out of the mine in the impoverished town of Monkayo during the search for the missing, said provincial police commander Senior Superintendent Albert Ferro.
It was not immediately clear how the tunnel became flooded early yesterday but there was heavy rain in the area at the time, Ferro told AFP.
Twelve miners were initially trapped. Two bodies were retrieved while five others were rescued and five are still missing, he said.
Deadly landslides are common in Monkayo in the west of the main southern island of Mindanao. But these have not deterred poor residents, some of them children, from working in the poorly-regulated mines.