Investigators stormed 20 charity shelters across two Malaysian states on Wednesday, arresting 171 suspects including religious studies teachers and caregivers, and bringing to safety over 400 children.
In what is believed to be the worst such case to hit Malaysia in decades, police suspect the victims -- aged from one to 17 -- had been subjected to sexual and physical attacks.
They were also allegedly forced by the care home staff to abuse each other.
Investigators were "working towards" further raids and arrests as the probe on the organisation called Global Ikhwan Services and Business (GISB) continued, said police inspector-general Razarudin Husain.
Investigations and health checks so far show that at least 13 minors had been sexually abused, Razarudin said at a press conference.
The children, who are temporarily being housed in a police training centre in Kuala Lumpur among other locations, are still undergoing medical examinations, added the police chief.
Razarudin had said on Wednesday that children as young as five were burnt with hot spoons, while others who were ill were not allowed to seek treatment until their condition became critical.
"The caretakers also touched the children's bodies as if to carry out medical checks," he said.
GISB has denied the allegations and said they do not run the care homes raided in the states of Selangor and Negeri Sembilan.
"It is not our policy to do things that go against Islam, and the laws," the group said in a statement this week.
Prime Minister Anwar Ibrahim said he has urged relevant authorities to "investigate thoroughly" without delay.
"This concerns the faith of the community. It is important and a serious matter, involving abuse of power, misuse of religion," he told reporters after performing Friday prayers.
The Selangor state government said they were going to "conduct regular checks" at religious schools to ensure there was no abuse and urged residents to contact the authorities if they had any information.
Multi-ethnic Malaysia has a dual-track legal system, with Muslims subject to sharia (Islamic law) in certain areas.
- DNA samples -
GISB has long been controversial for its links to the now-defunct Al-Arqam sect and has faced scrutiny by religious authorities in the Muslim-majority country.
Al-Arqam was banned by the authorities in 1994 for deviant teachings, while GISB members had in 2011 set up an "Obedient Wives Club" that called on women to be "whores in bed" to stop their husbands from straying.
According to its website, GISB says it is an Islamic company that runs businesses from supermarkets to restaurants, and operates in several countries including Indonesia, France and the United Kingdom.
Police believe the 402 minors in the care homes were all children of GISB members, Razarudin told AFP on Thursday.
"We feel that there's a need for DNA samples to be taken."
Religious authorities in Selangor state said this week they were closely monitoring GISB's activities.
"(We) remain vigilant about any facts leading to deviations from true Islamic teachings," they said.
The United Nations children's agency underlined the "unimaginable horror" faced by the victims.
The children "will need long-term professional medical and psychosocial support," said Robert Gass, UNICEF's Malaysia representative.
The case has also rattled locals.
"This incident is very shocking and sudden," said Uzair Abdul Aziz, 37, a Selangor resident.
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