Maqsood Ansari, 72, a former scientist with NEERI (National Environmental Engineering Research Institute) was nabbed after the 16-year-old girl filed a police complaint, alleging that the scientist has been abusing her since she was in Class 1.
The two younger girls - one aged 11 years and the other six-and-half-years - were being sexually abused also, she said in her complaint.
The man, she added, had offered to marry her, but also threatened all three of them against informing the authorities.
Ansari, the police said, was married at least twice, but could not father a biological child. Both his wives had left him.
After the eldest girl approached a non-profit through a friend's family, the girls were rescued by the police and shifted to a government shelter.
He has been charged with rape and under provisions of Protection of Children From Sexual Offences or POCSO Act.