The boy and other children had been whipped on the legs with a water hose by an assistant warden at their Islamic religious school in the state of Johor, just north of Singapore, district police chief Rahmat Othman told Reuters.
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Photos of him, legs blackened and swollen with infection, circulated online.
The boy was admitted to hospital two weeks later, slipping into a coma after doctors amputated both of his legs to prevent the spread of infection. The assistant warden was arrested on Saturday.
"We are now waiting for the medical and autopsy reports from the hospital before taking further action," Rahmat said.
The case has prompted calls for closer scrutiny of "tahfiz" schools, where students learn to memorise the Quran.
Such schools, child and education activists say, are mostly privately run and registered with state religious departments rather than the education ministry, which has strict guidelines on corporal punishment for students.
"To this day, we do not know who are actually in charge of regulating tahfiz schools," Noor Azimah Abdul Rahim, chairman of the Parent Action Group for Education, told Reuters.
Prime Minister Najib Razak, who on Tuesday announced a 30 million ringgit ($6.9 million) fund to develop tahfiz education, expressed his condolences.
"I would like the investigation into this case to be speeded up and for legal action to be taken if any offences were committed," he said on his Twitter account on Wednesday.
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The case follows controversy over a proposed bill that would have introduced stricter forms of the Islamic penal code, including punishments such as whipping.
Najib, who had previously expressed support for the bill, announced last month that the ruling coalition had decided not to table the bill in parliament.
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