The autopsy findings have come as a shock to people in the locality, 60km from Kerala capital Thiruvananthapuram.
Police had earlier treated the young girl's death as a suicide case. Now it will need to revisit this premise. For now, the police said they had registered a case of sexual abuse and sent her blood and viscera samples for further tests.
Her father told NDTV that he had all along insisted there was something horribly wrong. "I kept telling the police that my daughter will not commit suicide," he said, pointing that he suspected a relative was involved.
"I know my wife had to walk out of her parent's home with our daughter many times because she was abused there," he said.
The incident comes just weeks after a nine-year-old girl was found hanging in her home in Palakkad around 275km from Kollam. A little less than two months before her body was recovered, her 14-year-old sister was also seen hanging at the same spot.
The autopsy reports showed they had been repeatedly sexually abused.
After the issue was raised by the Opposition in Kerala Assembly, Chief Minister Pinarayi Vijayan ordered a Crime Branch probe into the sisters' deaths.