Below are the colleges which are offering agricultural and food engineering courses-

1- IIT, Kharagpur
2- Amity University, Noida
3- AMU
4- College of Technology and Engineering, Maharana Pratap University of Agriculture and Technology, Udaipur
5- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar
Govind Ballabh Pant University of Agriculture and Technology, Pantnagar.

To check all the colleges you can refer below link-

http://www.engineering.careers360.com/agricultural-and-food-engineering/colleges