The shocking incident came to light two days ago when the 8th standard student of a local school was seen crying and refused to go home even after school hours. When one of her teachers enquired, the petrified girl narrated her plight.
The school authorities immediately informed the police and a complaint was registered.
The girl's father, her 15-year-old brother and an uncle have been arrested, Thalassery Circle Inspector, M V Vinod Kumar, who is probing the case said.
The brother has been sent to juvenile home while the other two were produced in court and remanded to judicial custody.
The girl told police that she was sexually assaulted by the three since she was in her sixth standard.
According to Vinod Kumar, the victim has also told the police that her elder sister, who had committed suicide two years ago, had also been raped.
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Meanwhile, Kerala Vanitha Commission Chairperson, K Rosakutty told PTI that the incident was an 'insult' to Kerala's conscience.
The Commission would be writing to Chief Minister and Home Minister demanding re-enquiry into the case of the suicide of the victim's elder sister.
"This is a shocking case of two minor sisters being raped by family members. The elder sister, an 8th standard student, had committed suicide is the police version. But it needs to be probed as no proper inquiry was done then", she said, adding, both the cases were related.
As uncertainty looms large about the victim's future, the Commission was prepared to take her under its care, she said.
The victim has been presently housed at a home run by the Child Welfare committee. Efforts needs to be made to ensure that there were no interference in the case, she said.
Strongly condemning the incident, K Ajitha, president of "Anweshi", a women's organisation, said anti-rape case clinics needs to be set up in the state as early as possible.