"All accused have been arrested by the police. A team of police officials led by a woman IPS officer will probe the case. My government has taken cognisance of the incident," Fadnavis said in a statement.
The Chief Minister's statement, however, was silent on the exact number of the victims and the accused arrested so far.
State DGP Satish Mathur has said eleven persons have been arrested in connection with the case while search is on for remaining two.
An SIT has been formed to probe the case as the police suspect that more children could have been sexually exploited.
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The CM said, "A team of officials led by a woman IPS officer will probe the case. All directors of the ashram shala are being arrested."
Ashram shala is also known as tribal residential school in Maharashtra.
"Women police officers will visit all ashram schools, aided and government-run, in the state and speak to the girl inmates to find out whether laid down standard operating practices (SOP) related to security of the girls are being followed or not.
Earlier in the day, the DGP announced setting up of a Special Investigative Team (SIT), headed by a senior IPS officer, to investigate the case.
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Meanwhile, Maharashtra Tribal Welfare Minister Vishnu Savara announced revocation of the concerned residential school's recognition.
He also announced suspension of all the accused who are members of school staff and added that the case will be tried in a fast-track court.
"Children at this Ashram School will be accommodated in other Ashram Schools in the state," Savara said.