Fifteen female foetuses were found in drains in Beed in Maharashtra in 2009.
The 26-year-old pregnant woman's father had gone to the police station to complain about his son-in-law after his daughter's death.
Senior police officials in Sangli district said the remains were "buried with the intention of disposing them".
Dattatray Shinde, superintendent of police, said: "It appears to be an abortion racket".
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The Sangli police have also arrested Jamdade and registered a case against the absconder medico. "When the villagers suspected something fishy following the woman's death under mysterious circumstances, they approached police", Mr. Shinde said.
The woman was taken to the hospital by her husband Praveen Jamdade, who, despite objections of the father-in-law wanted his wife to abort the third girl child.
The main accused in the case, a homoeopathic doctor Babasaheb Khidrapure is absconding and police teams have been formed to trace him out, he added.
"This is awful. Female foeticide is occurring in the scale of a genocide in India".
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The Maharashtra government suspects that it is part of a cross-border abortion racket is in operation after 19 aborted female foetuses were found in the sewer.
Dr Ganesh Rakh, who campaigns to save the female child in India, said that the case is a clear example of how illegal sex determination and abortion is practiced in the country.
A report from British medical journal The Lancet in 2011 estimated there have been up to 12 million abortions of baby girls in India over the course of the last 30 years, with boys remaining the more favoured gender.
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