"We have built a cooperative relationship and going forward I would like to strengthen that," Prabowo told Kishida at a meeting in Tokyo.
resident-elect Prabowo Subianto on Wednesday told Japan's Prime Minister Fumio Kishida he wanted deeper security and economic cooperation just two days after telling Chinese President Xi Jinping he wished for close ties.
"We have built a cooperative relationship and going forward I would like to strengthen that," Prabowo told Kishida at a meeting in Tokyo.
Prabowo, who has previously said Indonesia was committed to a policy of non-alignment, visited Japan after travelling to China on Monday on his first foreign trip since his winning Indonesia's presidential election in February.
Both Tokyo and Beijing are courting Indonesia that ring the contested South China Sea, most of which China claims, to gain influence in the strategic region.
The current defence minister and former special forces commander will be sworn in by President Joko "Jokowi" Widodo in October.
His election has raised concerns among human rights groups who point to abuses he is alleged to have committed during his time in the military. Prabowo, who was found by a military council to have kidnapped student activists in 1998, denies the accusations.
Prabowo also met Japan's Minister of Defence Minoru Kihara in Tokyo.
Chinese President Xi on Monday praised ties with Indonesia on Monday, laying out a vision for regional peace as he met Prabowo amid tensions with other Southeast Asian neighbours.
Xi told Prabowo during talks in Beijing on Monday that bilateral ties "have entered a new stage of jointly building a community with a shared future", state broadcaster CCTV reported.
China "is willing to deepen all-round strategic cooperation with Indonesia and build a China-Indonesia community with... regional and global influence, so as to bring more benefits to the two peoples and make positive contributions to regional and world peace and development," Xi said.
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