Can one pursue MTech from an IIT in EC after completion of BTech Agricultural and Food Engineering from IIT ?
Definitely, each year many people switch their field of interest and take up a different branch in MTech than what they took in B.Tech. The only thing which you'll have to do is that clear the paper of GATE in EC and prepare well for the interviews, as the professors will be hell bent on knowing that why you want to switch you field, so keep your answer ready for these. Other than these you'll be good to go.
All the best!