Japanese Prime Minister Fumio Kishida demanded that Beijing provide an explanation "as soon as possible," calling the attack "extremely despicable."
The suspect, identified by his surname Zhong, stabbed the young child to death near his school in southern China. He was arrested by police immediately after the attack, officials said. The boy was enrolled at the Shenzhen Japanese School, as per the BBC.
China expressed its condolences to the family during a news conference on Thursday.
Lin Jian, China's foreign ministry spokesman, said the case was under investigation and that the two countries have been in communication.
"China expresses its regret and sadness that this kind of unfortunate incident occurred," the foreign minister told reporters, who later confirmed that the boy's father was a Japanese national and his mother was a Chinese national.
The motivation for the attack was not immediately apparent. However, certain observers have expressed concerns that the escalation of the nationalist sentiment in China may be resulting in an increase in violence against foreigners. There have been multiple stabbing attacks on foreigners in the country since June, some of them fatal.
Beijing has described these attacks as "isolated incidents," but the Japanese government refuted the claim and called on China "to prevent such incidents from happening again."
In the aftermath of the stabbing, a few Japanese schools in China reached out to parents, advising them to remain vigilant. The victim's school has suspended certain activities. Earlier this year, the Japanese government requested $2.5 million to hire security officers for school buses in China due to an increase in anti-Japanese attacks.