The deputy consul and the finance officer for the Chinese consulate in Cebu were killed, and the consul general was wounded, national police spokesman Wilben Mayor told AFP in a text message.
Two Chinese were arrested following the attack, one of whom is the husband of a diplomat at the consulate, Mayor said.
The other person arrested was a woman who also worked at the embassy, according to Mayor.
He said police retrieved a semi-automatic .45 Colt pistol from the scene.
The attack occurred at 1:30pm (0530 GMT) at a popular Cebu restaurant that serves Filipino food.
A spokeswoman at the Chinese embassy in Manila, Li Lingxiao, said she could not comment immediately.
“Our embassy is still verifying the facts. We’ll update you as soon as I have anything new,” Li said in a text message to AFP.
Philippine foreign ministry spokesman Charles Jose also said he had no comment, as authorities were still determining what happened.