The Philippines and China have engaged in frequent clashes in the crucial waterway, which Beijing claims in nearly its entirety despite an international ruling that its assertion has no legal basis.
The Royal Canadian Navy last year began taking part in joint maritime patrols in the area with its US, Australian, Japanese, and Philippine counterparts.
The visiting forces deal would allow Canadian troops to participate in joint exercises on land as well.
Canadian Defence Minister David McGuinty said the agreement would deepen the relationship with the Philippine military while advancing Ottawa's Asia-Pacific strategy, which calls for "a forward presence in the region".
"(We) will be moving forward on training fronts, on exchanges with our military colleges, information sharing, understanding cyber security," he told a joint news briefing in Manila.
He added that Canada hoped to take part in the archipelago nation's annual Balikatan military exercises next spring.
Manila, a US treaty ally, signed a visiting forces pact with New Zealand earlier this year and already had agreements in place with the United States, Australia and Japan.
A similar deal is in the works with France.
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