As I perceive and according to my opinion, following reasons are responsible for a low literacy rates of female in India even today:
Gender Discrimination in India
Big distance of school from Home.
Poverty.
Lack of physical facilities for girls, like toilet etc.
Scarcity of lady teachers.
Unwilling female teachers to work in rural locations.
The Govt. of India has taken some of the significant steps to tackle this. I have read about them online and listing them below:
Balika Samriddhi Yojana
Saakshar Bharat Mission
Beti Bachao Beti Padhao
Sukanya Samriddhi Yojana
kasturba Gandhi Balika Vidyalaya Yojna