Last week, China banned all seafood imports from its neighbour as Japan began releasing treated wastewater from the crippled plant in an operation the UN nuclear watchdog has declared safe.
Since then, Japan has urged its tens of thousands of citizens in China to keep a low profile and has increased security around schools and diplomatic missions.
Japan's foreign minister on Tuesday confirmed media reports that the brick was thrown at its mission and echoed calls from Prime Minister Fumio Kishida for China to calm the situation.
"We would like to urge the Chinese government again to take appropriate measures immediately, such as calling on its citizens to act calmly to prevent the situation from escalating, and to take all possible measures to ensure the safety of Japanese residents and our diplomatic missions in China," Yoshimasa Hayashi told reporters in Tokyo.
He added that China should "provide accurate information" about the Fukushima water release "rather than unnecessarily raising people's concerns by providing information without any scientific basis".
In Beijing, a spokesperson at the Japanese embassy told AFP that staff were "extremely worried".
"Some individuals have come to our (embassy) entrance," the spokesperson said.
"They took these kinds of actions, then were led away by armed police."
In response, foreign ministry spokesperson Wang Wenbin said Tuesday that Beijing "protects the safety" of foreigners in China, dismissing the "so-called concerns of the Japanese side".
"Ignoring the strong doubts and opposition of the international community, the Japanese government unilaterally and forcibly started the discharge of contaminated water from the Fukushima nuclear accident, which aroused strong indignation among people of all countries," he added.
"This is the root cause of the current situation."
- 'Don't speak loudly' -
Analysts say that China's sharp criticism of the Fukushima release is partly motivated by its geopolitical and economic rivalry with Japan.
On Sunday, Japan's foreign ministry urged its citizens in China to be "cautious in your speech and behaviour. Do not speak Japanese unnecessarily or too loudly."
Eggs and stones have also reportedly been thrown at Japanese schools in China.
Japanese residents in China vented their fears on X, formerly known as Twitter.
"I'm a bit scared... We have to worry about our own children being harmed by something we can't control. I don't know what to think," tweeted Miki, a Japanese woman living in Shanghai according to her profile.
A range of businesses in Japan, from bakeries to an aquarium, have also reportedly been subjected to thousands of crank calls that have included abusive and racist language.
Social media users in China have posted recordings and videos of the calls, some of which have attracted tens of thousands of likes.
Japan began releasing more than 500 Olympic swimming pools' worth of diluted wastewater from Fukushima into the Pacific on Thursday, 12 years after a tsunami knocked out three reactors in one of the world's worst atomic accidents.
All radioactive elements have been filtered out except for tritium, levels of which are within safe limits and below that released by nuclear power stations in their normal operation, including in China, plant operator TEPCO says.
Test results from seawater and fish samples near the plant since the start of the discharge -- which will take decades to complete -- have confirmed this, according to Japanese authorities.
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