Two people were killed and seven others missing in the Philippines after a tropical depression spawned huge waves and flash floods, forcing hundreds to flee their homes, authorities said Thursday.

Pre-emptive evacuation of people in areas prone to floods and landslides helped keep the casualties low, but others along the coast were hit hard by the storm, locally code-named "Queenie".

One woman was swept away by floodwaters on the central island of Cebu while a man was fatally injured when his boat was battered by huge waves off the island of Bohol on Wednesday, said regional disaster monitoring chief Olive Luces.

"Even before Queenie hit, we were already experiencing bad weather," she told AFP.

Four people went missing while at sea while three others were carried away by huge waves, Luces added.

The storm, with maximum winds of 55 kilometres (34 miles) per hour, hit the eastern coast of the southern island of Mindanao late Wednesday, then moved westward, across the central islands before heading to Palawan island.

It is expected to continue moving west towards the South China Sea.