Body of the girl was recovered from a plastic bag on May 23, they said.
Her father Kailash Chandra lodged his complaint at Dakshin police station alleging that she had been raped and murdered.
During investigation of the case, it was found that Kailash, who wanted a son, with the help of two exorcist Pramod Kumar and Diwaker Kulshresta murdered his daughter, police said.
Kailash and the two exorcists were arrested last night, they said.