The angry statement came despite China's efforts to soothe tensions over its South China Sea claims during a forum with ASEAN countries last week.
"We are strongly opposed to China's construction and operation of lighthouses on Cuateron Reef and Johnson Reef," said Charles Jose, a spokesman of the Department of Foreign Affairs.
"These actions are obviously intended to change actual conditions on the ground and aimed at bolstering China's territorial claim in the South China Sea. We will not accept these unilateral actions as a fait accompli," he added in a statement.
The two reefs are located in the Spratly islands in the South China Sea, a vital sealane and fishing ground which is claimed almost entirely by China.
China's claim conflicts with those of the Philippines as well as Brunei, Malaysia, Vietnam and Taiwan. All but Taiwan are members of ASEAN, the Association of Southeast Asian Nations.
The Philippines has been among the most vocal in criticising China's efforts to assert its claim over the waters, including its recent reclamation of land to transform isolated South China Sea outcrops into artificial islands that can host military facilities.
Manila has also filed a case with an international tribunal challenging Beijing's maritime claims.
In a forum with ASEAN defence chiefs in China last week, Fan Changlong, vice-chair of China's Central Military Commission, tried to ease tensions, pledging that his country would "never recklessly resort to the use of force, even on issues bearing on sovereignty".
However upon returning from the forum, Philippine Defence Secretary Voltaire Gazmin late Saturday reiterated the call for "rules-based solutions," to resolve the dispute.
"As responsible members of the international community, parties must refrain from unilateral actions that change the status quo and increase tensions," he said in a veiled criticism of China.
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