Biden and Kishida unveiled plans on Wednesday to restructure the US military command in Japan, the biggest such change since the 1960s.
The move is aimed at making US and Japanese forces more nimble in the event of threats, such as a Chinese invasion of Taiwan.
Biden insisted that the military upgrade in China's backyard was "purely defensive" but has made no bones about his desire to create alliances to counter Beijing.
In response to a question on Kishida's visit and the upgrade in ties, foreign ministry spokeswoman Mao Ning said the United States and Japan had "smeared and attacked China on Taiwan and maritime issues, grossly interfered in China's internal affairs, and seriously violated the basic norms governing international relations".
Mao said China was "strongly dissatisfied with and firmly opposed to this and has lodged solemn representations with relevant parties".
"The US-Japan relationship should not target or harm other countries' interests, and should not undermine regional peace and stability," she said.
- 'Peace and stability' -
A joint statement issued at the White House said the two sides wanted to upgrade their "command and control frameworks to enable seamless integration of operations and capabilities".
The United States has around 54,000 military personnel in Japan but they currently report to Indo-Pacific Command in Hawaii, around 6,500 kilometres (4,000 miles) away and a time zone 19 hours behind Tokyo.
The new framework will allow for greater "interoperability and planning" between the two countries' forces, the statement said, although details are yet to be finalised.
They said they plan to boost cooperation in intelligence, surveillance and reconnaissance as well as cybersecurity.
In Washington, Kishida hailed the alliance as crucial for upholding peace and democracy in the region, where China has been increasingly assertive, and called for "peace and stability" across the Taiwan Strait.
Mao insisted the "Taiwan issue is purely China's internal affair".
"We won't allow any interference from any external force," she said.
China regards Taiwan as its own territory and has never renounced the use of force to bring the self-ruled island under its control.
- South China Sea-
Biden will host the first trilateral summit between Japan, the Philippines and the United States later on Thursday to support Manila amid tensions with China in the disputed South China Sea.
The three countries conducted joint naval and air drills with Australia in the South China Sea at the weekend as they deepen ties to counter China's growing assertiveness.
China, in turn, conducted its own military "combat patrols" on Sunday.
Mao said China's activities "are in full compliance with international law and beyond reproach".
"China has indisputable sovereignty over the South China Sea Islands and their adjacent waters," she said.
"China will continue to properly handle maritime issues with relevant parties through dialogue and consultation and jointly safeguard peace and stability in the South China Sea."
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