In morning trade in Tokyo, shares in department store chain Takashimaya, and the owner of global fashion chain Uniqlo fell more than 5%.
Carriers Japan Airlines and ANA Holdings were also down.
Shares in Oriental Land, the theme park company that runs the Tokyo Disney resort, was around 5% lower.
The share price falls came after the dispute between Beijing and Tokyo has deepened in recent days.
On Sunday, the Chinese government urged its citizens to reconsider studying in Japan, citing risks to their safety and a rise in crimes targeting Chinese people.
China’s Education Ministry, external also told students already based in Japan to closely monitor the security situation.
Last year, more than 100,000 Chinese students were enrolled in educational institutions in Japan, according to a Japanese government survey.
Also over the weekend, Chinese airlines – including China Southern Airlines, China Eastern Airlines, and Air China – offered refunds for flights to Japan.
