"Given the worsened security situation in the Philippines, the consular department of the Ministry of Foreign Affairs urges Chinese citizens not to travel to the Philippines for the time being," a ministry statement said.
The warning came after three men were arrested last week over an alleged plot to bomb the Chinese embassy, the international airport and the business premises of ethnic Chinese tycoons.
In Beijing, foreign ministry spokeswoman Hua Chunying today urged the Philippine government to do more to protect Chinese citizens.
Philippine Justice Secretary Leila de Lima said last week that the bomb plot may be linked to a fringe politician who had been involved in a string of anti-Chinese protests.
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However the Philippine military dismissed the alleged bomb plot, calling the fringe politician a crank who posed no real danger and saying his "bombs" were merely firecrackers.
Police arrested him but then quickly released him.
Diplomatic relations between China and the Philippines have been extremely tense in recent years due to a dispute over competing territorial claims in the South China Sea.
Many foreign governments warn their nationals to avoid large parts of the southern Philippines due to the threats of kidnapping, however there are no blanket advisories similar to China's to avoid the entire country.
The travel warning was released just before reports emerged that armed men abducted an 18-year-old Chinese man on the strife-torn southern island of Mindanao late yesterday.
Local police spokesman Senior Inspector Leo Castillo said the gunmen had not been identified but it was believed to be another case of kidnapping for ransom, a common crime in the south committed by Muslim rebels.
However a spokeswoman at the Chinese embassy in Manila said today that diplomats were still trying to confirm if the abducted man was a Chinese citizen.
Chinese tourist arrivals in the first half of 2014 rose 13.6 per cent year on year to 2,26,163, the third highest, just behind South Koreans and Americans, according to the Philippine government.