The judicial probe was ordered a day after Odisha Police "ruled out" possibility of any rape despite the minor girl's claim that she was gang raped by four persons in uniform on October 10.
A district judge will inquire into the alleged gang rape case under the provisions of the Commission of Inquiry Act, 1952, an official statement issued by the chief minister's office said.
Patnaik had earlier directed the Crime Branch of Odisha Police to investigate the matter.
Several activists and the girl's family members had rejected the police version and expressed displeasure over the way the medical examination of the minor girl was conducted.
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While the girl's family members had demanded a judicial inquiry, opposition BJP sought a CBI probe into the matter after the police claimed that the girl, who studies in class nine was not raped.
"Medical and scientific experts were engaged to find out the truth. During the course of the investigation, the movement of the security forces, who were allegedly involved in the case, could not be established" Odisha DGP R P Sharma yesterday said.
Pratap had said, "As per the doctors' opinion, there is no such evidence of gang rape or rape of the minor girl."
"I have discussed the matter with all the medical experts treating the girl at Kunduli, Jeypore in Koraput district and at the MKCG Medical College Hospital in Berhampur during the course of the investigation," he said.
The alleged gang rape of the tribal girl has sparked outrage in the state with the opposition parties staging protests, demanding justice for her.