The three institutions - none is in the top 25 - are the Indian Institute of Technology, Kharagpur (30th), followed closely by IIT Bombay (joint 33rd) while IIT Roorkee takes up the 56th place.
There are 15 countries in the Asia top-100 list. The University of Tokyo is Asia's number one institution in the list where Japan (22 universities), Taiwan (17), mainland China (15) and Republic of Korea (14) are the best represented nations.
"In India, there has clearly been a serious pressure on spending per student, given the huge expansion of student numbers in the recent years. There is a well established shortage of qualified faculty in the Indian university system," Phil Baty, editor of Times Higher Education, told HT.
There has also traditionally been a discord between university research and research and development in industry, which usually works in tandem, Baty said, adding: "Improving the quality of research will be India's challenge."
Pawan Agarwal, a higher education adviser to the Planning Commission, says: "Rapid growth in the face of staff shortage and declining per-student spending has affected standards. Improving quality has rightly been prioritised in the 12th plan".