Japan also agreed to provide 43.6 billion yen ($318.25 million) in loans to Indonesia for use in infrastructure projects and disaster prevention, Reuters reported.
Japanese Prime Minister Fumio Kishida said on Wednesday he and President Joko "Jokowi" Widodo had agreed during talks to cooperate in a variety of fields, including energy and maritime security.
Japan also agreed to provide 43.6 billion yen ($318.25 million) in loans to Indonesia for use in infrastructure projects and disaster prevention, Reuters reported.
At the outset of the meeting in Tokyo, Kishida told Jokowi that Japan hopes to work with Indonesia to realize a free and open Indo-Pacific region, a vision that Japan is pursuing amid China's rise.
Jokowi, meanwhile, conveyed his condolences over the death of former Prime Minister Shinzo Abe earlier this month, saying the late former leader helped advance bilateral relations to a strategic partnership, Kyodo News reported.
The two leaders were expected to discuss security and economic cooperation between the two countries as well as the upcoming G-20 summit, where Russia's invasion of Ukraine is almost certain to top the agenda.
The president, on the second leg of his three-nation tour after China, will chair this year's G-20 summit in Bali in November. Indonesia has invited both Russian President Vladimir Putin and Ukrainian President Volodymyr Zelensky to the gathering.
During his fourth visit to Japan as president, Jokowi is also scheduled to meet with Emperor Naruhito later in the day before leaving for South Korea.
Japan and Indonesia will celebrate the 65th anniversary of diplomatic relations next year, while also marking the 50th anniversary of friendship between Japan and the Association of Southeast Asian Nations.
In recent years, Japan and Indonesia have been boosting cooperation in security. For the first time, the Japanese Ground Self-Defense Force is scheduled to join a multinational joint exercise in Indonesia in August.
Indonesia and the United States have also invited other nations including Australia and Singapore to take part in their annual military exercise, as China's rise raises security concerns in the Indo-Pacific region.
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