Bratstar Pariong (30) of Mawlaisyiem village committed the crime taking advantage of the mental condition of the girl, they said.
While the minor girl lives with her family at the village, she would visit her uncle's house often, the police said quoting an FIR lodged by the girl's family yesterday.
The accused, who is yet to be arrested, had also threatened the victim with dire consequences if she reported the matter to anyone, the police said.
On examination by doctors at the Nongstoin Civil Hospital where she was taken for a check-up following a complaint of abdominal pain, it was found that she had been raped and was in an advanced stage of pregnancy.
In another incident, the police has announced an award of Rs 20,000 to anyone providing information leading to the arrest of two men who allegedly raped a seven-year-old girl last month at a nearby forest at Malki, near here.
Meghalaya, which has a matrilineal society, recorded 179 rapes in the past one year out of which 118 cases are of minors.