The boy's father Ravi Prakash in his police complaint said his son fell ill after taking a poisonous substance on September 15, upset over his class teacher allegedly punishing him.
The boy died during treatment in a hospital on Wednesday, police said.
His family members later found a note in his bag in which he blamed the class teacher, police said.
A case has been filed against the teacher Bhawana Joseph and she has been arrested, police said, adding the school management has been named in the case.
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