Six Chinese ships have sailed into waters around a disputed archipelago, with Beijing saying they were there for "law enforcement" around islands Japan nationalised earlier this week.
The move, dubbed "unprecedented" by Tokyo, came on Friday as it was reported Japanese nationals had been physically attacked in China, marking the latest stage in a deteriorating row between Asia's two biggest economies.
Japanese living or visiting China were warned to take extra precautions after assaults and harassment were reported to the consulate in Shanghai, a base for Japanese businesses and a popular tourist destination.
Tokyo summoned the Chinese ambassador to protest what it insists is an incursion into territorial waters around islands it controls, called Senkaku, but claimed by Beijing as Diaoyu.
Al Jazeera's Marga Ortigas, reporting from Hong Kong, said protesters in Beijing have called for a boycott of Japanese products to defend their country’s interests.
The latest tension surfaced after Yoshihiko Noda, the Japanese prime minister, announced that Japan is buying the disputed private islands and transferring control to the government.
Commentators say Noda's solution, nationalising the islands and continuing its policy of doing nothing with them, was an attempt to navigate between rising nationalism at home and China's growing assertiveness on the oceans.
"We'll do our utmost in vigilance and surveillance," said Noda when asked about Japan's response to the latest move by China. He also established a task force to deal with the issue.
Fujimura's comments come as the Japanese consulate in Shanghai reported physical attacks on its nationals.
"A group was dining late at night, and they were harassed and assaulted by Chinese," said a statement on the consulate's website.
The consulate said bottles were thrown at some Japanese, and drinks and food were poured over others, while one person reported having a pair of glasses broken.
Japan's foreign ministry has warned its nationals who are in China or who are planning to visit there to be aware of anti-Japanese demonstrations and to avoid drawing attention to themselves.
The embassy in Beijing said Japanese should avoid approaching the building, where protests have been reported, unless absolutely necessary.
Diplomats say Tokyo and Beijing would prefer to keep the row from spiraling out of control and harming deep economic ties.
China, the world's second-largest economy is Japan's biggest trading partner with mutual trade in 2011 growing 14.3 percent in value to a record $345bn.
A Nissan Motor Company executive has said the tensions were already affecting business with China.
But with China facing a once-in-a-decade leadership change and an election looming in Japan that the ruling party looks set to lose, managing the row could be harder than in the past.
"The last thing China wants is to affect the trading relationship," Andrew Leung, a Hong Kong political analyst told Al Jazeera.
"But China has got no choice but to use these means because there’s no way China would confront America militarily, but also, China cannot be seen to be backing down."
The uninhabited islets were at the centre of a chill between Beijing and Tokyo in 2010, after Japan arrested a Chinese trawler captain whose boat collided with Japanese Coast Guard vessels near the area.
Sino-Japanese relations have long been plagued by China's bitter memories of Japan's military aggression in the 1930s and 1940s and present rivalry over resources and regional clout.
"Ultimately, though, China needs the region to remain peaceful and stable to continue to progress, and it risks isolation if it alienates its neighbours," Al Jazeera's Ortigas said.