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© Gethin Chamberlain for the ObserverTanuja, 11, Priya, 5, and Prachi, 9, the three sisters found in a well, raped and murdered.
As the nation still struggles to come to terms with the attack on a Delhi student, another disturbing sex abuse case has shaken a rural community. It has raised awkward questions about police efficiency, disputed evidence and local gossip

Priya was the vivacious one, a bright five- year-old who loved music and wanted to be a teacher. Prachi was quiet, nine years old and painfully shy; Tanuja more headstrong, an independent 11-year-old.

The three sisters were Madhuri Borkar's only children. On 14 February they left home for schools in the village of Murmadi as usual. When they failed to return on time the family went to the police to report the girls missing.

"Go away," the police told them. "Come back tomorrow if they don't turn up." No one knows if the girls were still alive at that point. But it was two more days before a farmer found their bodies floating in the dark water at the bottom of a deep well in a corner of a paddyfield one mile from their home.

Even then, police initially treated the deaths as an accident. It was not until villagers started blocking the highway in protest that they started to pay attention. Two days later, the results of the postmortem examination came through and the story exploded. The girls had been raped and murdered, the report said. In the febrile atmosphere that has gripped India since the gang rape of a 23-year-old Delhi medical student last December, the case was taken up as another indictment of the plight of India's females.

Then, just as suddenly, the rest of the country seemed to lose interest. "Do rape cases make national news only if they take place in metros [metropolitan areas]?" the CNN-IBN TV network asked plaintively. The answer appeared to be yes. There has been a series of cases since the Delhi student's death. Only last week a seven-year-old girl was raped and murdered after vanishing from a wedding outside the city of Kanpur in Uttar Pradesh. It attracted little attention nationally, while the rape of a seven-year-old girl in Delhi provoked violent protests and made international headlines.

National figures released last week show rape cases rising year on year in India (although activists say the 24,206 cases recorded in 2011 are the tip of the iceberg and that police routinely fail to take complaints seriously). At the same time, conviction rates are falling, down from 44.3% in 1973 to 26.4% in 2011.

Even against this difficult background, what has become known as the Bhandara rape case has proved particularly challenging. The only indisputable facts are that three young girls are dead and that the police did not take their disappearance seriously. Even the question of rape has been muddied by disputes over postmortem and forensic findings.

Such was the initial official indifference to the disappearance of the Borkar sisters that, more than two weeks after they vanished, no one is even sure how they died. It was not until Friday that India's home minister, Sushilkumar Shinde, felt compelled to address parliament on the case, expressing revulsion at "the ghastly rape and murder".

Initial suspicion fell on people from outside the village. But with no arrests and no obvious external suspects, the girls' family have found themselves the subject of local gossip, newspaper speculation and background briefings intended to place them firmly in the frame. Madhuri Borkar is said to be HIV positive: the death of her husband, Jaipal Raibhan Borkar, in 2008 was attributed to Aids. Suspicions have been voiced about the involvement of Borkar's in-laws and the girls' cousins and about possible winners and losers in the family's financial affairs. There have been questions asked about the behaviour of Tanuja, said to have been seen carrying money and wearing new clothes not provided by her family. Neither has Borkar herself escaped scrutiny, with questions raised about her character.

Her father-in-law, Raibhan Ganpat Borkar, 65, says the family are not listening to "gossip". But when Borkar herself claimed that her mother-in-law, Sataya Shela, had previously tried to poison the girls and had been torturing her since the death of her husband, it only served to strengthen the conviction of many in the area that the Bhandara rape was not an outside job.

Only a court can ultimately decide. But Borkar, 29, will make a convincing witness. She sits in a brown plastic chair in the blue-painted front room of the home she shares with the family of her late husband, dabbing at her tears with the end of her blue-and-grey floral sari.

"Priya loved music and playing with her toys," she says. "She was in the first grade. She was clever and grasped things quickly and understood things. She wanted to be a teacher. Even when we used to quarrel, she was so understanding that she never minded my cross words. She used to hold my cheeks and convince me not to be angry with her."

The single-storey family home sits on a narrow lane a few hundred yards from the younger girls' school. The front door is open; outside, a line of police carrying riot helmets files past.

Borkar recalls the last time she saw her daughters. "I had prepared some leftover rice and fried it and gave it to them for their lunch. But Priya said she didn't want to go to school without a proper lunch, so I made her some chapatis and brinjal and she ate it and left the house happy because I had prepared separate food for her."

Prachi was a quieter child, she says. "She loved to eat fruit and to ride her bicycle. She didn't talk very much, she used to be quite silent. She was not very good at studies. I think she was a bit timid. She used to get frightened about even small things."

Tanuja was the opposite, she says. "She used to look after herself, comb her own hair, travel to school alone. She was very independent, though she used to take care of her little sisters and they used to play together. I think they used to love me very much, more than anyone else.

"They used to ask me to stand in the corner of the room and they would dance and they would ask me to judge which one was the best and to give them a prize. I couldn't choose one though, so I used to give them all prizes, money to buy some chocolate."

The first indication that something was amiss was when the girls' friends dropped off their schoolbags at the house, but Borkar says she assumed they would soon return. "I thought they might be playing somewhere so I didn't think to worry, but about 6pm I started thinking that something was strange. I searched at the houses of their friends but they were not there." So the children's grandfather went with neighbours to the local police station to report the girls missing. But instead of starting a search, the police sent them away.

"I didn't have a husband and I don't think they took me seriously," Borkar says quietly.

The delay in starting the investigation left police so little to work with that they have resorted to offering 100,000 rupees (£1,211) - a large sum in a rural area - in an attempt to flush out witnesses.

It seemed that Tanuja had gone to her sisters' school on the afternoon of 14 February and asked them to leave with her. The belief is that someone persuaded the older girl to take her sisters to the field by the well with the promise of treats and that the children were then attacked.

The village of Murmadi lies in the Bhandara district of Maharashtra state, about 578 miles north-east of the state capital, Mumbai. The well where the bodies was found is about 200 yards off the highway, just visible from the road. The well is deep, with only a low lip, and the water is a long way down.

But the crime scene has offered few clues. There were empty alcohol bottles near the well and chocolate wrappers. But it rained on 15 February and any footprints or vehicle tracks were washed away.

Even the conclusions of the postmortem have come under scrutiny, with a subsequent forensic report challenging the original rape claims. But Dr Dinesh Kuthe, one of the doctors involved, insists there is no doubt that the girls had been sexually assaulted. "There were injuries to the genitals and there was bleeding," he said.

The cause of death remained a mystery though, he said, and there was no water in the lungs to indicate drowning. "We think that some people killed them before throwing them into the well," he said. "If there were signs of what happened, they vanished in the water."

Borkar has given the Observer written permission to name the girls and to carry their photograph as a reminder of what is in danger of being lost amid the claims and counterclaims over this rural tragedy; that three beloved little girls are gone.