Police suspect it to be a case of murder and have not ruled out the possibility of sexual assault, an official said, adding that they are awaiting postmortem report.
The body was spotted lying near a farm in Dhamane village, around 15 kms away from Chakan, by the girl's brother last morning.
The official said the teenager went missing on Friday afternoon after she left for her home in the village from her family farm.
"On Friday, the girl and her mother were working in their farm when the girl received a call from her female friend and left for (her) home to meet the friend. The girl's mother asked her to bring water while returning to the farm," said Chakan Police Station inspector Manoj Yadav.
He said when the girl's mother returned home in the evening she found her daughter missing.
Mr Yadav said the mother and her 19-year-old son then inquired with their neighbours and came to know that she was seen going towards farms around 3.30 pm (on Friday).
"The family members of the girl and villagers searched for her in the vicinity and near the farms, but couldn't trace her. Subsequently, they approached police and lodged a missing and kidnapping complaint," the police inspector said.
Mr Yadav said it was the brother of the girl who spotted her body lying near their own farm. "The deceased was semi-naked and her head was found smashed with a heavy stone while her tongue was stuck between her teeth," said Mr Yadav.
He said police found the mobile phone and parts of clothes of the girl some 100 metres away from her body. "We suspect sexual assault but are awaiting her postmortem report," the officer said.
Police have questioned around 30 labourers who work in small industries near the village in connection with the incident.
A case has been registered under IPC sections related to "kidnapping, murder and causing disappearance of evidence".
"Appropriate sections will be added if the sexual assault is confirmed in the postmortem report," Mr Yadav said.