Japanese Foreign Minister Toshimitsu Motegi and Defence Minister Nobuo Kishi held the talks with German Foreign Minister Heiko Maas and Defence Minister Annegret Kramp-Karrenbauer via video conferencing.
In the East China Sea, Beijing claims a group of uninhabited Japanese-administered islets, and the dispute has long troubled bilateral relations.
Two U.S. carrier groups conducted joint exercises in the South China Sea on Tuesday, days after a U.S. warship sailed near Chinese-controlled islands in the disputed waters, as China denounced the United States for damaging peace and stability.
In Beijing, Chinese Foreign Ministry spokesman Wang Wenbin said the frequent moves by U.S. warships and aircraft into the South China Sea in a “show of force” was not conducive to regional peace and stability.
The busy waterway is one of several flashpoints in testy Sino-US relations, with the United States continuing to challenge Beijing's territorial claims in the contested waters.
US relations with China deteriorated under former US President Donald Trump over a variety of issues including the pandemic, Chinese policies in Hong Kong, Beijing's treatment of its Muslim minority and trade.
A U.S. aircraft carrier group led by the USS Theodore Roosevelt entered the South China Sea over the weekend to promote “freedom of the seas” at a time of U.S. concern about China-Taiwan tensions and Beijing asserting its maritime agenda.
Taiwan, meanwhile, reported an incursion of Chinese bombers and fighter jets into its air defence identification zone.