Chinese rules which took effect this month require foreign fishermen to seek Beijing's approval to operate in the disputed waters.
Department of Foreign Affairs spokesman Raul Hernandez said the Philippines asked China to clarify the edict and was told by Beijing that it was "an implementation of China's fisheries law" and that the region was under Chinese jurisdiction.
China claims virtually the entire South China Sea, putting it at odds with Brunei, Malaysia, the Philippines, Vietnam and Taiwan, which also claim parts of the busy waters as their territory.
The United States has criticised the Chinese regulation as "provocative and potentially dangerous." China has asked Washington to stay out of the Asian dispute.
The Philippines and Vietnam are among the most vocal critics of China's claims over the disputed waters, saying they infringe on their own 200-mile (322-kilometre) exclusive economic zones.
China and rival claimants have beefed up their navies and stepped up patrols in the disputed territories, increasing the risk of confrontation.
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