The World Wide Fund for Nature reported outbreaks of crown-of-thorns starfish in at least seven coastal areas. One starfish can consume six square meters (60 square feet) of healthy coral reef in a year.
Outbreaks of the starfish, also known as Ancathaster planci, are detected every summer - March-May - when local ocean temperatures and nutrient levels increase, giving rise to algal blooms.
"Normally, reefs should be left alone to deal with unusual occurrences such as this," WWF said in a statement. "However, the situation facing Philippine reefs is far from normal."
It said major predators that should, under normal conditions, keep crown-of-thorns starfish in check are steadily declining due to illegal collection for food and the aquarium trade.
A recent World Bank study revealed that barely 1 percent of the Philippines' 25,000 square kilometers (9,650 square miles) of coral reefs remain pristine and more than 50 percent are unhealthy.
WWF advised people involved in cleaning up crown-of-thorns starfish not to touch them. Their long spines can sting and inflict severe swelling, pain and nausea that can last for hours or days.
Tongs should be used to gently pry the starfish from the coral head or rock face. The starfish should be burned in an open space; cutting them up could allow them to regenerate, it said.
Ultimately, the best response is to keep the reef healthy, stop overfishing, manage sewage and agricultural runoffs, and promote balanced reef biodiversity, WWF added.