The child had his legs amputated on Friday to stop an infection and underwent surgery on Saturday because of congealed blood in one of his hands, the newspaper reported.
His aunt told the New Straits Times newspaper that doctors at a hospital in Kuala Lumpur have been monitoring a blood clot in his left shoulder.
If it remains, he will have to have his arm amputated, she said.
The boy and 14 of his classmates are believed to have been beaten with a water hose on 24 March for making too much noise in the school's assembly building, police say.
His diary said that if one student made an error at the school in Kota Tinggi, in southern Malaysia, the whole group would be punished.
It said they would often volunteer to be beaten first, so they could try to sleep before waking for prayers at three in the morning.
The Federation of National Associations of al-Quran Tahfiz Institutions (Pinta), an umbrella group for religious schools, said it had seen CCTV footage which showed the boy being beating on the soles of his feet.
But Pinta's president, Mohd Zahid Mahmood, told reporters the public should not to jump to conclusions about the case but allow the authorities to complete their investigation.
The government has promised to take a closer look at religious schools, which are exempt from many state inspections.Published: 2017-04-26 10:03:37