The girl's mother suspected her daughter might be pregnant only last week and took her to a doctor.
Reports said the girl was often left at home when her mother went to work.
She told her mother that she had been repeatedly raped by her stepfather, who had warned her not to say anything.
India's Supreme Court has received several petitions from rape victims in recent months requesting terminations and each case has been referred to a panel of medical experts.
India has a gruesome record on rape. New Delhi alone registered 2199 rape cases in 2015, an average of six a day.
Nearly 40,000 rape cases are reported every year but the real number is thought to be much higher, as victims are wary of how their complaints will be dealt with or the social stigma attached to sex crimes.
