The boy was stabbed on his way to school at about 8 a.m. on Wednesday, local time, by the suspected 44-year-old assailant, who was arrested on the spot, according to Chinese authorities. The child died in the early hours of Thursday, Japanese foreign minister Yoko Kamikawa told reporters.
"I take the incident extremely seriously," Kamikawa said.
"This should never happen in any country. Particularly, I sincerely regret that this despicable act was committed against a child on his way to school."
Japan has asked China to provide a detailed explanation of the facts and to take strong safety measures, she added.
Authorities in both Japan and China declined to disclose the nationality of the victim, while the website of the Shenzhen Japanese School says it is for children of Japanese nationality. Japan does not recognize dual citizenship for adults.