Suspected Chinese hackers defaced the website of the Philippines News Agency (PNA) on Sunday, officials said, a possible repeat of cyber-attacks last year also blamed on China during a territorial row.
The state-run agency's website temporarily displayed the Chinese flag and the text: "China Hacker EvilShadow Team, We are evil shadow. We are the team. We have our own dignity China Hacker Lxxker."
Asked if Chinese hackers were behind the attack, presidential spokeswoman Abigail Valte said an investigation was pending but added: "The note left on the site tends to invite that conclusion."
Another government spokesman, Herminio Coloma, said the hackers group shared news of the attack via Facebook.
"The site is working again now," Coloma told reporters, but did not say how long it had been down. He added authorities were attempting to track down the group and had beefed up cyber security in the wake of the attack.
The hacking came days after Philippine authorities arrested 12 suspected Chinese poachers whose boat ran aground in a protected coral reef in the Sulu Sea, which is well within the country's territory.
The incident came amid damaged bilateral relations due to overlapping territorial claims to the South China Sea.
Last year, cyber-attacks on several government websites were blamed on Chinese hackers during a standoff in Scarborough Shoal, a group of rocky outcrops in the South China Sea that is close to main Philippine island of Luzon.
China claims virtually all of the South China Sea on historical grounds, including waters close to the shores of its neighbours.
The Philippines, as well as Vietnam, have accused Beijing of becoming increasingly aggressive in staking its claims, stoking potential confrontations.