The cache of some 300 creatures, which included squirrel-like sugar gliders, wallabies and a threatened species of cockatoo, was one of the nation's largest wildlife busts.
"In terms of live animals, this was likely one of our biggest [captures]," said government environment official Rogelio Demelletes.
Four suspects were arrested in the raid that turned up animals native to Australia, Indonesia and Papua New Guinea.
The haul also included seven red birds of paradise and 26 Moluccan cockatoos, which wildlife monitor IUCN considers to be at high risk of extinction in the wild.
Philippine officials put the market value of the confiscated creatures at US$192,000 (HK$1.5 million), which is more than all the live wildlife seized by Manila last year.
As the global convention on wildlife trade lists the Moluccan cockatoo as a species threatened with extinction, the suspects face up to 12 years in prison if convicted under the country's wildlife act.
Despite the law, the Philippines has a burgeoning trade in wildlife transacted on social media platforms.