The Department of Foreign Affairs said in a statement that the plans should be condemned by the international community because they violate maritime domains of countries in the region and impede freedom of navigation.
Chinese state media announced the plans, saying southern Hainan province, which Beijing says administers the South China Sea, had approved laws giving its police the right to search vessels that pass through the waters.
Last week the Philippines, Vietnam, Taiwan and India protested a map on a new Chinese passport that depicts disputed areas as belonging to China.
The Philippine statement said it wants Beijing to "immediately clarify its reported plans to interdict ships that enter what it considers its territory in the South China Sea."
It said Manila was concerned that ships entering waters claimed by China, which is "virtually the entire South China Sea ... can be boarded, inspected, detained, confiscated, immobilized and expelled, among other punitive actions."
China's action will be "illegal and will validate the continuous and repeated pronouncements by the Philippines that China's claim of indisputable sovereignty over virtually the entire South China Sea is not only an excessive claim but a threat to all countries," the statement said.
The maritime territorial disputes include the Spratly Islands over which China, the Philippines, Vietnam, Malaysia, Taiwan and Brunei have conflicting claims. The Spratlys chain is believed to sit atop rich oil and gas reserves and straddles one of the world's busiest sea lanes.