A hundred yards from a school playing field on the edge of Nayagarh, a small town in eastern India, is an innocuous damp circular patch covered with what appears to be sticks and stones.

A closer look reveals that the debris is shards of tiny skulls and bones, all that remains of more than 40 female foetuses - aborted because of their sex and then dumped in a disused well.

The secret tragedy of being conceived female in India burst into the open this week with the grim discovery of the well, dug on land earmarked for a private hospital - the Krishna clinic owned by an obstetrician, Nabakirshora Sahu, and his wife, Savitha. The latter is in custody but the medic is on the run.

Last Thursday Santish Mishra, a health official, was poking at the top of the hole, from which had been exhumed 132 bags of putrefying human remains. Above the grisly sight hangs an acrid smell, the telltale chemical stench of hospital waste used to hide the truth.

"Femur, skull, forearm - probably. We are pretty sure these are all female, aborted at about five months which is the legal limit," said Dr Mishra. "You can say it was a hidden mass grave."

In India ultrasound technology, coupled with a traditional preference for boys, has led to mass female foeticide. Although gender-based abortion is illegal, parents are choosing to abort female foetuses in such large numbers that experts estimate India has lost 10 million girls in the past 20 years. In the 12 years since selective abortion was outlawed only one doctor has been convicted of the crime.

Nursing homes

Authorities in Nayagarh said they will come down hard on clinics offering ultrasound scans to determine the sex of an unborn child and the "nursing homes" where abortions are carried out. All five clinics and eight nursing homes have been shut and sealed.

It is hard to believe that in such a small town illegal terminations could happen without official connivance - at least one government doctor has been arrested.

Two weeks ago an 11-year-old boy out playing in a grove at the edge of Nayagarh town opened a sealed bag to find bloody remains of seven female foetuses. Although the alarm was raised and local television stations aired shocking images, by the time the police arrived - three hours late - they had been removed.

"I was very scared. There was blood everywhere," said Upendra Kalasha, the boy who found the remains. "The people came but not the police."

Paresh Nayak, the top local civil servant, said: "Nobody said anything to me. The public have a responsibility to come forward. They did not and we were overtaken by events."

One of those events was the election of India's first female head of state, president Pratibha Patil. In her inaugural address this week to both houses of parliament she said India "must banish (the) social evil of female foeticide".

What happened in Nayagarh is merely the tip of the iceberg. Last month a doctor in Delhi was arrested after remains of aborted babies were found in a septic tank at his practice. In February police found the remains of 15 infants buried in the backyard of a hospital in the central state of Madhya Pradesh. A television investigation last year filmed dozens of doctors offering to perform illegal terminations of female foetuses and dump them in rivers or in fields.

The prejudices against having a daughter run deep in India, where tradition dictates that when she is married a woman's family must pay the groom's family a large dowry. By contrast a son is considered an asset. Even leaving aside the wealth his bride will bring, a boy will inherit property and is seen as a way of securing parent-care in old age.

Development has not erased traditional values: in fact, selective abortion has been accelerating in a globalising India. Wealthier and better-educated Indians still want sons. A survey revealed that female foeticide was highest among women with university degrees. The urban middle classes can also afford the ultrasound tests to determine the sex of the foetus.

"We are seeing a rush of multinational companies selling ultrasound machines in India with little regard for how they are used," said Sabu George, a campaigner against female foeticide. "Chinese companies now sell machines at just 200,000 rupees (£2,500) half the price of American ones. Every small town doctor can get one and more families can afford the test."

The mix of old customs and new technology means a shortage of girls that will haunt India for decades, say researchers. The latest figures from a sample registration system which covers 1.3m households shows that for the two years up to 2005 Indian had just 880 female babies born to each 1,000 males.

Prem Chowdhry, who has studied the implications of a widening gender deficit, says unmarried young men are turning to crime and violence against women has increased. Some men in the rich northern state of Haryana have taken to buying brides from other parts of India. Many of these wives end up slaves and their children are shunned.

"We are seeing five to 10 households in every village where wives are brought," said Professor Chowdhry. "The pattern is being reproduced across India and we are staring at a huge problem for the future."

· The following correction was printed in the Guardian's Corrections and clarifications column, Friday August 3 2007. Indian tradition does not usually dictate that when a woman is married her family must pay "the groom's in-laws" a large dowry, as we said in the article below. We meant to say that the dowry goes to the groom's family. This has been corrected.