Japan will provide equipment such as rescue boats and supplies under the official security assistance deal, signed by the two countries' foreign ministers on the sidelines of a Tokyo summit marking 50 years of ties between Japan and the Association of Southeast Asian Nations (ASEAN).

Japanese Prime Minister Fumio Kishida welcomed the elevation of the Japan-Malaysia relationship to a 'comprehensive strategic partnership,' Japan's foreign ministry said in a statement.

In addition to Malaysia, ASEAN members the Philippines, Vietnam, Indonesia, Malaysia and Brunei claim parts of the South China Sea disputed by China, which claims almost all the waterway that is a conduit for more than $3 trillion of annual ship-borne commerce. The Permanent Court of Arbitration in 2016 said China's claims had no legal basis.

China and Japan last week accused each other of maritime incursions after a confrontation between their coast guards in waters around islands they both claim in the East China Sea.

Japan's aid to Malaysia follows similar deals with the Philippines and Bangladesh this year and is part of a plan announced in April for Japan to provide developing countries with financial assistance to bolster their defenses.

In the three-day summit through Sunday, Japan is offering ASEAN members support to boost their standing as international actors and help them manage their relations with others, including China, said an official at Japan's foreign ministry.

Kishida is expected to meet separately with the leaders of all the ASEAN members, which also include Cambodia, Singapore, Thailand, Laos and Timor-Leste.