After a meeting with President Benigno Aquino III in the Philippine capital, Abe announced that Japan will provide a concessional loan to build 10 coast guard patrol boats for the Philippines.
The Philippines has already received two coast guard ships from the United States as it seeks to build a deterrent naval force after China took control of a disputed shoal off the northwestern Philippines last year.
China's assertiveness to lay claim to most of the South China Sea after decades of relative calm has alarmed Manila, which has turned to the United Nations to seek international arbitration. Beijing has indicated it won't cooperate.
In a statement issued after their meeting, Aquino said that the two leaders reviewed security challenges both countries face and promised to cooperate to push for "responsible action from international players," in a reference to China.
He said that maritime cooperation with Japan was a pillar of the countries' strategic partnership.
Abe said that a key element of Japan's efforts to revive its economy and promote regional peace and security lies in closer relations with the 10-member Association of Southeast Asian Nations.
ASEAN includes the Philippines and Vietnam, both of which have disputes with China in the South China Sea.
Abe's trip to Manila was the last leg of a three-day visit to Southeast Asia that also took him to Malaysia and Singapore.
At a news conference, Abe sounded conciliatory toward Beijing, saying problems are inevitable among neighbors but that Japan's ties with China are important and based on "common strategic interests."
He urged China to view the relationship the same way and to be open to "frank and candid" talks, without preconditions. He said he has directed his foreign affairs officials to "promptly" set up meetings with their Chinese counterparts.
Abe also said there were "deepening discussions on what is the appropriate form of constitution for the present-day Japan" based on the global security environment. The Japanese constitution, crafted by the U.S. at the end of World War II, renounces war and prohibits Japan from maintaining forces with "war potential."
He said there would also be discussions on the national defense program guidelines and Japan's right of "collective defense."
On Friday, an interim Defense Ministry paper released by the Japanese government called for increased military capabilities and a more assertive role in regional security.
The implementation of some of the changes outlined in the paper would be a major policy shift for the military, which is limited to self-defense and banned from overseas combat operations under Japan's pacifist constitution.
Abe assured countries in the region occupied by Japanese forces during World War II that constitutional reforms would be made "with the obvious premise of pacifism, people's sovereignty and basic human rights."
Abe's visit to Southeast Asia came after Japan scrambled jets on Wednesday to keep watch on a Chinese Y-8 early warning plane flying over international waters between Japan's southern Okinawa island and an outer island relatively close to the disputed area in the East China Sea.
The Chinese Defense Ministry issued a statement defending the right of its aircraft to operate in the area.
Around the same time the Chinese jet was sighted, Japan's coast guard reported the appearance of four Chinese coast guard vessels near the disputed islands, called Senkaku by Japan and Diaoyu by China.
On Friday, China said that ships from its newly formed coast guard confronted Japanese patrol vessels and "sternly declared" China's sovereignty over the islands.
The uninhabited archipelago is controlled by Tokyo but also claimed by Beijing.
Chinese coast guard ships have also been spotted this week at Mischief Reef off the western Philippine coast, according to a confidential Philippine government report obtained by the Associated Press. China occupied the vast reef in 1995, sparking protests from rival claimant Manila.
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