The Zhongguancun Second Primary School in Haidian District said in a statement it was, however, "filled with remorse" for what had happened and "deeply sorry for hurt to the student and his parents."
It insisted that "the incident was accidental and did not constitute bullying or violence."
School campus CCTV footage from November 24 shows the fourth-grade boy being followed into a toilet by two of his classmates. Less than a minute later, the two classmates can be seen running back to their classroom.
The school said the fourth grader had been in the toilet for 72 seconds, while his two classmates were in there for 30 seconds, state-run Xinhua news agency quoted him as saying.
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There are no cameras in the toilet, however, the faculty was told by the three students that one child emptied a trash can over the forth grader from the adjacent cubical, just, in their words, "to tease him," while the other classmate laughed.
The school claims that the three students had a normal relationship at school and there was "no apparent conflict."
However, the boy's parents insist that his classmates had acted in malice and they should be punished. They also filed for compensation.
The boy's mother published an open letter last week, describing how her son had been bullied for almost a year, and that he now suffers from acute stress disorder, which is characterised by severe anxiety and means he is too unwell to attend school.
The school confirmed that the child had been absent since December 2.
The mother's open letter has been shared over 100,000 times on WeChat, and read over 6 million times on Weibo within days of being posted.
Disclaimer: No Business Standard Journalist was involved in creation of this content