The training, characterised by Japanese media essentially as a show-of-force exercise, coincided with renewed tensions in the region after North Korea's latest ballistic missile launches earlier this week.
The aircraft carrier USS Carl Vinson and the guided missile destroyer USS Wayne E. Meyer from the US Navy joined the Japanese destroyers Sazanami and Samidare in the East China Sea to "increase proficiency in basic maritime skills and improve response capabilities," the US Navy said in a statement.
Japan's Maritime Self-Defense Force, the country's navy, said in a separate statement that the exercises focused on "tactical training", without elaborating
But Japan's conservative Sankei Shimbun newspaper said the drill was aimed at issuing a warning against nuclear-armed North Korea by "exhibiting the strength and deterrent power of the Japan-US alliance."
The joint drill commenced a day after North Korea launched four ballistic missiles on Monday, with three landing provocatively close to Japan, which the US is obligated to defend under a security treaty.
Pyongyang has claimed the launch was a training exercise for a strike on US bases in Japan and supervised by leader Kim Jong-Un.
Seoul and Washington are separately carrying out annual joint military exercises in South Korea.
The Japan-US training was also meant to display their joint presence in the East China Sea, where Japan and China are locked in a long-running dispute over uninhabited islets, the Sankei said.
In Japan they are known as the Senkakus, while China claims then as the Diaoyus.
Successive US administrations have assured Japan that the islands fall under their security treaty, meaning if they are attacked the US will defend them.
The Carl Vinson was expected to join the South Korea-US drills after the exercise with Japan, the Sankei said.
The two sets of exercises come as US Secretary of State Rex Tillerson is set to visit South Korea, Japan and China next week for his first trip to the region since he became President Donald Trump's top diplomat.
The US Pacific Command said Monday that the Americans had begun deploying the THAAD anti-system to South Korea, which is designed to defend the US ally from a North Korean attack.
The deployment has outraged Pyongyang ally China, which strongly opposes it as a challenge to its security ambitions in the region.
China responded that it was "firmly opposed" to the deployment and vowed to "resolutely take necessary measures" to defend its security interests.
China has argued that the deployment would further destabilise the situation on the Korean peninsula.
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