Philippine President Ferdinand Marcos Jr witnessed the ceremony in Manila, where Defence Secretary Gilberto Teodoro Jr and and his New Zealand counterpart, Judith Collins, inked the Status of Visiting Forces Agreement.
The treaty sets the legal framework to allow military engagements of both nations, including joint drills in each other's territory and other co-operative activities. It has been approved by New Zealand officials, but still needs to be ratified by the Philippine Senate for it to take effect.
China has frowned on the security alliances being pursued by the Philippines, one of the staunchest allies of the United States in Asia, under Marcos.
When the Philippines signed a similar agreement with Japan in July, China's Foreign Ministry said the region did not need "military blocs, let alone small groupings that instigate bloc confrontations or a new Cold War."
Philippine officials said then that China has no business meddling with their domestic affairs.
"These partnerships have become very important in the face of all that is happening," Marcos said during Wednesday's ceremony.
Ahead of the signing, Collins said in a statement that "we are committed to reinvigorating our security relationships, to playing our part and working with regional partners such as the Philippines to uphold the international rules-based order."
Teodoro told The Associated Press last month the Philippines would continue to build security alliances with other friendly countries to deter China's aggression.
China's hostile actions, Teodoro said, should be regarded as a global threat because they could eventually restrict movement in the South China Sea, a key global trade route crucial for global supply chains.
China claims virtually the entire South China Sea and has deployed coast guard and navy fleets and suspected militia ships to guard what it says is its territory and airspace. It has used water cannons and dangerous blocking manoeuvres against Philippine coast guard and fisheries vessels in the disputed waters, causing collisions and injuries on a number of occasions.
Vietnam, Malaysia, Brunei and Taiwan also lay claims that clash with China's, but territorial confrontations have particularly flared between Beijing and Manila in the last two years.
The Philippines has visiting forces agreements with the US and Australia, which has been participating in large-scale combat exercises between American and Filipino forces that include live-fire exercises in or near the South China Sea and in northern Philippine islands just a sea border away from southern Taiwan.
