Hello Piyush,

For the admission in the Indian Institue of Astrophysics, one must have a minimum required eligibility which is M.Sc.(Physics)/Integrated M.Sc. (Physics)/B.Tech/B.E./M.Tech/M.E. with minimum 60% marks from class 10. 
So, you just cannot apply for Ph.D. after your BE, you must complete your PG as well before giving the NET exam, and then when you secure JRF you can apply for the admission.

Hope this helps,
Good Luck!