The strike group is in the region as tensions spike over North Korea's rogue arms programme and concerns that Pyongyang is planning a sixth nuclear test as it pursues its goal of a weapon capable of reaching the US mainland.
The Carl Vinson drills are expected to last several days and involve two Japanese warships, Japan's defence ministry said.
It is the third time the Japanese navy has held exercises with Carl Vinson after two such drills in March.
Washington has sought to clarify the aircraft carrier's whereabouts in recent days after President Donald Trump suggested it was steaming towards North Korea when in fact it was sent towards Australia.
US Vice President Mike Pence on Saturday said it would soon arrive in the Sea of Japan, days after vowing an 'overwhelming and effective' response to any North Korean attack.
He has also renewed calls for China to use its 'unique' position to bring Pyongyang to heel.
Pyongyang has ramped up its rhetoric in recent weeks, threatening to hit back against any provocation.
It has also renewed threats against regional US allies, including Japan and South Korea, which both host large American military contingents.
"Seeing the threats we are facing now, it is no surprise that Japan and the United States conduct joint exercises," a senior lawmaker of Prime Minister Shinzo Abe's ruling party told Japan's NHK public broadcaster, adding the exercises would send a "strong message".
Washington is sending a senior envoy on the nuclear stand-off with North Korea to Tokyo this week for talks with his Japanese and South Korean counterparts.
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