The agreement was ratified by a vote of 16-4, Philippine TV network GMA News reported.
Under the agreement, 95 percent of Philippine exports to Japan will be entitled to zero duties. Ten years from its effectivity, tariffs will be removed on almost all industrial goods.
"In one short sentence, my word is my bond," Senator Panfilo Lacson said when explaining his "Yes" vote.
Last month, Senator Miriam Defensor Santiago, chair of the Senate foreign relations committee, released to the other lawmakers copies of the exchange of notes between the foreign affairs chiefs of Japan and the Philippines to guide them in ratifying the controversial treaty.
She said that in international law, "an exchange of notes constitutes a treaty, binding on the parties and implying performance in good faith."
"This exchange of notes will in effect constitute an integral part of the treaty," she said.
President Gloria Macapagal-Arroyo signed the agreement with then Japanese Prime Minister Junichiro Koizumi in September 2006 in Helsinki during the European leg of her four-nation trip.
