Two diplomats were killed and a third wounded in a shooting at a restaurant in Cebu City on Wednesday.
Police have taken a woman who works at the consulate and her husband into custody.
They have diplomatic immunity and will be sent back to China.
The suspected shooter was identified by police as Li Qing Liang. Mr Li's wife, Guo Jing, who works in the consulate's visa section, was also held for questioning.
Beijing has invoked the couple's diplomatic immunity under the United Nations' Vienna Convention, foreign ministry spokesman Charles Jose said.
The 1961 Vienna Convention spells out protections afforded to diplomats and embassy staff, including immunity from local laws and criminal prosecution.
China says it is investigating the shooting.
The deputy consul and the finance officer for the Chinese consulate in the city were killed and the consul general wounded, police said.
The consul general, Song Ronghua, who was celebrating his birthday at the restaurant, is in a stable condition after being shot through the neck.
"We're still trying to determine the motive for the shooting," said Chief Superintendent Prudencio Banas.
The consul general's deputy Sun Shen was shot in the neck and finance officer Li Hui was shot in the head, police said.
A handgun has been recovered from the scene, police spokesman Wilben Mayor told AFP.
The attack occurred at 13:30 (05:30 GMT) at Lighthouse, a popular restaurant.
Restaurant manager Stephen John Patero said the shooting occurred in a private room, which is a favourite among local politicians.
He said waiters who served the diners heard the guests shouting at each other before the shots were fired.
"They are all friends who apparently figured in an argument," he said.
The Philippine Foreign Ministry has said it will give China custody of the two suspects involved in the killing of two Chinese diplomats in the Philippines.