The breeder of the dogs, has to register the pups by sending a fee to the Kennel club of India. You can contact the breeder / owner and ask him to register the pup for you, that is if the parents are registered with the kennel club of India in the first place.Tell him you will bear the charges if that is an issue, but first make sure they are KCI registered.
The second option is to contact the kennel club of your area who is part of KCI and you can then register your dog with unknown parents when he is older. They will advise you regarding the procedure etc. Visit the KCI website and get the Hyderabad number from them.
Hope the above is of help.