I want to control a motor remotely over the internet using a GSM/GPRS module with a data connection.
Do you have a link to the device in question?
Is it possible for me to establish a direct client-server type link using gprs and send instructions to the arduino to control the motor?
What do you mean by "direct"? Typically, client/server links are stateless. That is, the client contacts the server for some data, and the server responds with that data. The server then promptly forgets that is has ever heard from that client.
If the motor is connected to the server, this should be fine, as long as there are not a lot of clients trying to control the same motor. Presumably, you will put something in place to prevent this from happening, or design the motor-controlled device so that is doesn't destroy itself when abused (and it will be).
How to do this project depends a lot on the GSM/GPRS shield you plan to use and where you are.