Scholz is on his second trip to Japan in less than a year, and came with six ministers for government-to-government talks as Berlin works to boost its profile in the Asia-Pacific region, and ahead of the G7 summit being hosted this May by Japan in Hiroshima.
There were few concrete results outlined by the leaders, but both stressed the need to strengthen and diversify supply chains hit by everything from the pandemic to Russia's invasion of Ukraine.
"In our conversations about economic security, we talked about beefing up supply chains," said Kishida.
Both nations want to strengthen "their influence in strategic sectors, including mineral resources, semiconductors and batteries, and share best practices to address risks," he said.
Bitten by its reliance on Russian energy since the invasion of Ukraine, Germany has been battling to pivot away from other economic dependencies, in particular on China.
It has also been ramping up overtures to Asian nations including Japan, Indonesia and India, as it tries to diversify its supplies and exports alike.
Scholz said relations with Japan had been raised to a "new level" in Saturday's talks and that both countries were keen to learn the "right lessons" from the economic dependencies revealed by pandemic disruptions and the war in Ukraine.
Kishida, who is in the midst of a diplomatic blitz including talks with the leaders of South Korea and India, said the war in Ukraine had made it all the more important for Japan and Germany to step up security cooperation.
A joint statement issued by the defence ministers of both countries said they would work on new deployments by Germany's military in the region, as well as joint exercises.
They also pledged "a legal framework facilitating joint activities" by both militaries.
Scholz said the German military would carry out a tour of the Asia-Pacific region "in coming years".
German and Japanese fighter jets carried out joint exercises in Japan last September.
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