Japan is increasingly positioning itself as Indonesia’s primary strategic partner in the Indo-Pacific region, marked by a significant deepening of bilateral cooperation in defense, energy, and other key strategic sectors over the past 12 months. This evolving relationship was underscored by the meeting between Japanese Prime Minister Takaichi Sanae and Indonesian President Prabowo Subianto, who walked past an honor guard at the Akasaka Palace in Tokyo on March 31, 2026.
The convergence of interests between Jakarta and Tokyo highlights a new phase in their relationship. Indonesia, as Southeast Asia’s largest economy, seeks partnerships that can bolster its security and economy while upholding its non-aligned foreign policy. Japan, in turn, aims for an expanded role as a regional security provider, complementing its established economic presence in Southeast Asia. Indonesia’s control over vital straits—Malacca, Sunda, Lombok, and Makassar—and its abundant natural resources synergize well with Japan’s expertise in defense, manufacturing, and emerging technologies.
Defense cooperation has become a prominent aspect of this expanding partnership. On June 7, authorities from both countries agreed to initiate discussions regarding the export of Japan’s older Asagiri-class destroyers to Indonesia. This followed a defense cooperation agreement signed just one month prior, which included the potential acquisition of Japanese submarines and the newer Mogami-class stealth frigates for Indonesia.
Energy security also stands as a crucial pillar of the growing ties. Indonesia’s ambition to diversify its energy mix, including a desire to develop up to 500 MWe of nuclear capacity by 2034, aligns with Japan’s need for reliable long-term energy partners, aiming to generate 20 percent of its energy from nuclear sources by 2040. In mid-March 2026, Indonesia and Japan signed a memorandum of cooperation focused on developing nuclear energy technologies and securing the critical minerals supply chain. This initiative came shortly after the two countries, alongside the U.S., hosted a conference on developing small modular reactors (SMRs) to enhance nuclear energy cooperation. The discussions aimed to support Indonesia’s long-term clean energy and energy security goals, reinforcing its role as a regional leader in nuclear reactor development. Previously, Indonesia received assistance from the U.S. State Department’s civil nuclear energy security assistance program and collaborated with Oregon-based NuScale in early 2023 on SMR deployment, facilitated by a U.S. Trade and Development Agency grant.
Beyond defense and energy, cooperation efforts have expanded into various other areas. On June 5, Japan and the World Health Organization announced an initiative to address Indonesia’s existing immunization gaps. In April 2026, Indonesia and Japan agreed to cooperate on carbon investment and facilitate knowledge exchange in forestry and conservation. Around the same time, the government-affiliated Japan External Trade Organization hosted a Japan-Indonesia Business Forum with the Indonesian Chamber of Commerce and Industry in Tokyo to foster further economic cooperation, including investment partnerships specifically for Indonesia’s sovereign wealth fund, Danantara. In late 2025, a cooperation agreement was signed focusing on the utilization of local currencies for all bilateral transactions, aiming to reduce costs and exchange risk while boosting trade and investments.
Despite this progress, the growing relationship faces challenges. Political uncertainty in both nations, including declining approval ratings for Japanese Prime Minister Takaichi Sanae and economic uncertainty in Indonesia, along with the arrest of Indonesia’s top anti-corruption prosecutor, could complicate long-term policymaking. Public opinion in Indonesia also presents a hurdle, with some viewing Japan as being too closely aligned with the United States, raising questions about compatibility with Indonesia’s long-standing non-aligned foreign policy.
For Japan to solidify its position as Indonesia’s principal Asian partner, Tokyo must demonstrate that increased cooperation genuinely strengthens Indonesia’s national sovereignty and strategic flexibility. If this balance can be maintained, the Indonesia-Japan partnership is poised to become one of the most significant in the region in the coming years.
