The announcement came after authorities recently seized a large number of protected animals during a raid on a home in Manila, China's official Xinhua news agency reported.
The newly formed Philippine Operations Group on Ivory and Illegal Wildlife Trade will file criminal charges against the suspected owners of the confiscated animals, Environment Secretary Ramon Paje said.
The raiding team recovered 78 myna birds, 12 parrots and five juvenile crocodiles in the operation, but all were dead, officials said.
"What's particularly alarming about this poaching incident is that there were reports that most of these endangered animals were intentionally killed to avoid detection by authorities, and such act carries a higher penalty," Paje said.
Under Philippine law, illegal trade of endangered species is penalized by a fine of $4,610 and a jail term of two years, while the killing of endangered animals carries the penalty of six-year imprisonment and a fine of $11,500.
Paje condemned the killing and insisted the government "won't tolerate such cruelty to animals."
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