Trapping, selling or exporting geckos, regarded by some Asians as cure-alls, is punishable by hefty fines and jail terms of up to four years, Environment Secretary Ramon Paje warned in a statement.
"The law expressly provides that the collection, trade or transport of geckos without appropriate permits... is punishable by imprisonment of up to four years and a fine of up to 300,000 pesos (about $7,000)," he said.
Paje said the 300-gramme (10.6-ounce) tropical reptiles, known for their flamboyant skin hues and sticky footpads, now sold for 50,000 pesos each in a lucrative Asian market.
Population declines in the wild in countries such as Malaysia have forced traders and suppliers to source the carnivorous, usually night-feeding lizards from countries such as Thailand and the Philippines, Paje said.
Some folk healers in the Philippines are known to advise asthma sufferers to drink tap water sprinkled with pulverised, fried geckos.
"They play an important role in maintaining our fragile ecosystems," Paje said of the lizards, which mainly feed on insects and worms as well as moss.
Twenty-six gecko species are found only in the Philippines, which also has eight other varieties that are also found elsewhere, he added.
Some of the larger species hunt small birds and rodents, the ministry said.