The "canonical" way to do this on Unix-y systems is with the sudo command. It's far more secure because you can specify which users can execute which commands, and also demands the user's own password -- thus there's no need to hand out the root password.

You don't specify which flavor of Unix you're using, but take a look at your docs and see if sudo is included. If it is, you can use either system or exec or some othe way to access it, depending on what you're doing.