The map depiction by China is reported to be in the form of a U-shaped "nine-dash line" in the passports, which the Philippines says covers its territory. China's continuing sovereignty claims to much of the vital sea has raised international concerns.
"The Philippines strongly protests the inclusion of the nine-dash lines in the e-passport as such image covers an area that is clearly part of the Philippines' territory and maritime domain," Foreign Affairs Secretary Albert del Rosario said in his country's protest note handed to the Chinese Embassy in Manila, the Manila Bulletin reported.
"The Philippines does not accept the validity of the nine-dash lines that amount to an excessive declaration of maritime space in violation of international law. ... The Philippines demands that China respect the territory and maritime domain of the Philippines."
Government officials said the Chinese action was a violation of the Declaration on the Conduct of Parties in the South China Sea, which Beijing signed in 2002 along with the 10 members of the Association of Southeast Asian Nations that includes the Philippines. The declaration calls for the signatories to "refrain from actions that complicate and escalate the dispute."
The South China Sea is a vital sea lane for global commerce and other activities and some of neighboring nations, with decades-long overlapping territorial claims to the resource-rich islands in the Sea, strongly object to China's stand. Those nations include the Philippines, Vietnam, Malaysia, Brunei and Taiwan.
The Financial Times reported Vietnam also has raised the passport issue with Beijing.
Philippines's GMA News said the latest development stemmed from Beijing's release of a new batch of e-passports. Vietnam and the Philippines already have had separate incidents with China over the dispute.
"We are expecting a reply soon" to the protest, the report quoted Philippines Foreign Affairs spokesman Raul Hernandez as saying.
The Philippines says the region in the Sea, which it calls the West Philippine Sea, including the waters, islands, rocks and other maritime features, form an integral part of the Philippine territory and maritime jurisdiction.
GMA News quoted Hernandez as saying Manila cannot just ignore China's passport action. "The passport will be used by Chinese nationals and if they carry that kind of map that violates our sovereignty and if we allow that then it would mean acquiescence to their claim of the whole of South China Sea," he said.
At the recently concluded East Asia Summit, Philippine President Benigno S. Aquino III urged all participants to respect the exclusive economic zone and continental shelves of all coastal states, irrespective of their size or naval power, the Philippine Information Agency reported. He said such a step would also comply with the provisions of the Declaration on the Conduct of Parties in the South China Sea.
Aquino also called on all territorial claimants to jointly discuss the maritime claims and resolve the disputes in accordance with the U.N. Convention on the Law of the Sea.
"At no time in the contemporary history of the South China Sea has clarification and delimitation of maritime areas become more urgent and imperative than they are now," he said.
The summit was also attended by U.S. President Barack Obama during his three-nation Asia tour.
Speaking at the same summit, Chinese Premier Wen Jiabao was quoted by the official Chinese media as saying the disputed Scarborough Shoal in the South China Sea is an integral part of Chinese territory and China's sovereignty over them is indisputable. China refers to the Shoal as the Huangyan Island.
China has insisted on bilateral negotiations with related parties to resolve the issue, while the United States prefers a multilateral approach. Critics of the bilateral approach say it would allow China to influence those with whom it has economic ties.
Last July, the Chinese military set up a garrison in its newly created Sansha City in south Hainan province, which is seen as being designed to strengthen its claims.
Wen was quoted by Xinhua as saying China's stance on the South China Sea issue is clear and consistent, and that China, as a continental and maritime country, attaches importance to the peace, stability, free navigation and security in the South China Sea.