• Indian Institute Of Technology, Kharagpur
• Indian Institute Of Technology, Roorkee
• Vellore Institute Of Technology
• Indian Institute Of Technology, Guwahati
• National Institute Of Technology, Warangal
• PSG College Of Technology, Coimbatore
• National Institute Of Technology, Durgapur
• Manipal Institute Of Technology
• BMS College of Engineering, Bangalore
• Chaitanya Bharathi Institute of Technology, Hyderabad
• PES Institute of Technology, Bangalore
• SASTRA University, Thanjavur
• National Institute of Technology, Raipur
• GITAM University, Visakhapatnam
• Karunya University, Coimbatore
• Sathyabama University, Chennai
• Acharya Institute of Technology, Bangalore
• Dr B R Ambedkar National Institute of Technology, Jalandhar

You can check the top colleges below for Biotechnology Engineering

Indian Institute of Technology, Roorkee

Indian Institute of Technology, Delhi

Indian Institutes of Technology, Guwahati

School of Life Sciences, University of Hyderabad, Hyderabad

Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala

School of Chemical and Biotechnology, Sastra University, Thanjavur

Department of Biotechnology, SRM University, Tamil Nadu

GGS Indraprastha University, Delhi 

Good Luck!!