The three were found dead with gunshot wounds in the city of Bacolod on Tuesday, the official said.
Of the three, two were male and one female, with one victim found with tied hands. Another also had traces of being hand-tied with tape, the official explained.
A local embassy official was sent to the scene to figure out the exact circumstances of their deaths, he added.
The latest death report brought the number of South Korean nationals killed in the Philippines to six this year, including a missionary found dead in his home in May.
Last year, a total of 11 Korean nationals were killed in the Philippines. (Yonhap)