China claims almost all of the South China Sea, despite an international ruling in 2016 concluding this has no legal basis.
US President Donald Trump and Japanese Prime Minister Shigeru Ishiba said on Friday they opposed China's "unlawful maritime claims, militarisation of reclaimed features, and threatening and provocative activities in the South China Sea" after they met in Washington.
Chinese foreign ministry spokesman Guo Jiakun hit back saying: "The China-related content of the US-Japan joint statement blatantly interferes in China's internal affairs, attacks and smears China and exaggerates regional tensions".
China had "lodged solemn representations" with both countries, he added at a regular press briefing.
Friday's meeting was the first between Trump and Ishiba, who both heaped praise on the other and doubled down on decades-old ties in security and trade.
Japan is one of the United States' closest allies in Asia, with around 54,000 US military personnel stationed in the country.
Beijing has in recent months pressed its territorial claims in the South China Sea -- which overlap Malaysia, Vietnam, Indonesia, Brunei, the Philippines and Taiwan's -- more stridently.
It has deployed navy and coast guard vessels in a bid to bar the Philippines from strategically important reefs and islands in the area.
The Philippines and United States are bound by a mutual defence pact, and the recent clashes have sparked fears the US military could be drawn into an escalation.
In January, US Secretary of State Marco Rubio voiced "serious concern" over what he called Beijing's "coercive" moves in the South China Sea and Taiwan, during his first call with Chinese counterpart Wang Yi.
China claims democratic, self-ruled Taiwan as its territory and has not renounced the use of force to claim it.
Trump and Ishiba said in their joint statement that they support Taiwan's participation in international organisations and "opposed any attempts to unilaterally change the status quo (in the Taiwan Strait) by force or coercion".
Like most countries, the United States has no official diplomatic relations with Taiwan, but it is the island's main supplier of arms for defence.
Guo warned the United States and Japan on Monday to "clearly oppose Taiwan independence".
"If the relevant countries really care about peace and stability in the Taiwan Strait, they should abide by the one-China principle and clearly oppose Taiwan independence," he said.
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