Senior police officials in Sangli district said the remains were "buried with the intention of disposing them".
The police told the BBC that they found the foetuses while they were investigating the death of a woman who had undergone an illegal abortion.
Activists say the incident proves yet again that female foeticide is rampant in India despite awareness campaigns.
The police said that the woman had died in a "botched abortion", and they were looking for the foetus near a local hospital when they made the grisly discovery.
"It appears to be an abortion racket. We have arrested the husband of the woman, and have launched a manhunt for the doctor who has gone missing," Dattatray Shinde, superintendent of police, told the BBC.
Similar cases have come to light in the past.
Eight female foetuses were found in 2012 in a plastic bag near a lake in Indore city in the central Indian state of Madhya Pradesh.
In June 2009, 15 female foetuses were found in drains in Maharashtra's Beed district.
Dr Ganesh Rakh, who campaigns to save the female child and appeared in the BBC's Unsung Indians series, said the recent case proves that illegal sex determination and abortion was still practised in India.
"This is horrifying. Female foeticide is happening at the scale of a genocide in India. This case proves that people still prefer boys and girls are still unwanted," he said.
"I think abortions were happening on a large scale in Sangli. Once the doctor is arrested, I fear we will find more aborted female foetuses."
Sex-selective abortion and sex-determination tests are illegal in India, where there is a widespread social preference for boys.
Police in the western Indian state of Maharashtra have found 19 aborted female foetuses near a hospital.