Biden and Prime Minister Fumio Kishida released a joint statement covering collaboration in spheres from space to semiconductors, but the crux of the document was defense.
The "new era of US-Japan cooperation" is aimed at better countering an assertive China, the two leaders said, and comes as long-pacifist Japan hikes defense spending, acquires counter-strike capabilities and brings all its forces under one command.
What have the countries agreed?
There are around 54,000 US military personnel in Japan but currently they report to Indo-Pacific Command in Hawaii, around 6,500 kilometers (4,000 miles) away and 19 hours behind.
The joint statement issued at the White House said the two sides want to "bilaterally upgrade our respective command and control frameworks to enable seamless integration of operations and capabilities."
Details will be hammered out, but the new framework will "allow for greater interoperability and planning between US and Japanese forces in peacetime and during contingencies."
Where will they deepen cooperation?
The pair also said they would create a new forum between their defense ministries for discussing policies to "better integrate and align our defense industrial policy, acquisition, and science and technology ecosystems."
That would involve "co-development and co-production of missiles" and maintenance of US military ships and aircraft at Japanese commercial facilities, they said.
The nations plan to boost cooperation in intelligence, surveillance and reconnaissance as well as cybersecurity.
They will also explore creating a humanitarian assistance and disaster relief hub in Japan, the statement said, without giving further details.
The statement also touted several existing initiatives, including a deal for Japan to buy long-range Tomahawk missiles from the United States and US plans to relocate an air base in the southern region of Okinawa.
Are other countries involved?
Other countries in the region are also alarmed by Chinese activities. On Thursday, Philippine President Ferdinand Marcos, Kishida and Biden will hold their first trilateral summit.
The US-Japan statement also set out a "vision to cooperate on a networked air defense architecture among the United States, Japan and Australia to counter growing air and missile threats."
The AUKUS security partnership -- the United States, Australia and Britain -- is "considering" cooperating with Japan on advanced defense technology, the two nations said, echoing a previous AUKUS statement.
Britain announced it will take part in regular joint military exercises with Washington and Tokyo starting in 2025, which Wednesday's statement welcomed.
Japan joined the United States, Australia and the Philippines for military drills in the South China Sea at the weekend that riled Beijing.
How important are the new announcements?
James Brady of the Teneo risk consultancy told AFP that while the "guiding principle clearly remains that of deterrence," the agreements should help the pair respond to regional security threats.
"In operational terms, harmonized changes to the command and control frameworks should make the two sides' militaries more prepared than ever to deal with a future contingency in the region -- be that with China or North Korea," he said.
"It would not be an exaggeration to say that this visit marks the all-time high-water mark of US-Japan relations," Brady added.
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