Prabowo, currently Jakarta's defence minister, met Chinese President XiJinping on Monday, his first visit to a key trade partner since he won thepresidential election held in February.
At those talks, Beijing said it was "willing to deepen all-round strategiccooperation with Indonesia".
Prabowo then travelled to Tokyo where he met Kishida.
During their meeting on Wednesday Kishida "stated that Japan attached greatimportance to cooperation with Indonesia in maintaining and strengthening thefree and open international order based on the rule of law", Japan's foreignministry said.
He added that "Japan would advance security cooperation with Indonesiabesides the provision of a large patrol vessel for Indonesia decided inDecember 2023," the ministry said.
The terms "free and open" and "rule of law" are often used by the UnitedStates and its allies including Japan to make a veiled reference tocountering China's increasing assertiveness in the Asia-Pacific region.
China is one of the biggest sources of foreign direct investment in Indonesiaand has poured billions of dollars into projects in the archipelago nation, reports BSS.
Tokyo's foreign ministry said that "president-elect Prabowo expressed hisgratitude for Japan's assistance to date and his hope to further enhancebilateral cooperation in a broad range of areas including security,agriculture and fisheries as well as disaster prevention".
Prabowo is now on his way to Malaysia, according to the Indonesian defenceministry