South Korean President Yoon Suk Yeol and his Philippine counterpart Ferdinand Marcos met in Manila and agreed to closer ties between their coast guards.
Yoon said they will strengthen "tackling transnational crime, information sharing and conducting search and rescue missions."
"We shared a common understanding about the importance of peace, stability and safety in the South China Sea," Yoon told reporters after the bilateral meeting.
"Our two countries will continue to work together in order to establish a rules-based maritime order and for the freedom of navigation and overflight pursuant to the principles of international law in the South China Sea," he added.
South Korea has repeatedly commented on tensions in the disputed waters.
In March, Seoul expressed its "grave concern" over China's "repeated use of water cannons against the Philippine vessels" in the area.
China has for years sought to expand its presence in contested areas of the South China Sea, brushing aside an international ruling that its claim to most of the waterway has no legal basis.
It has built artificial islands armed with missile systems and runways for fighter jets, and deployed vessels that the Philippines says harass its ships and block fishing.
Cooperation agreements signed in the bilateral meeting Monday cover areas such as critical raw material supply chains, as well as a feasibility study on reviving the Philippines' mothballed Bataan Nuclear Power Plant.
"As the geopolitical environment is only becoming more complex, we must work together to achieve prosperity for our peoples and to promote a rules-based order," the Philippines' leader Marcos said ahead of the meeting.
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