Your choice to do an MBA is good considering how much of a preferred course it is currently for engineering graduates. But, I don’t think there is any MBA program specialising in Computer Science. Maybe, you can do an MBA in IT or Systems management which are related fields and would keep you in a good position to become an IT manager of a firm who also has a good understanding of the administrative side of things and thus this can be said to be the best possible combination for a graduate of computer science who is interested in pursuing an MBA. Also, you can check out foreign universities like Stanford which offer a very flexible course and thus you can pursue subjects from CSE too while you do your MBA.
Hope this helped!