If your system supports it, look into Pluggable Authentication Modules - PAM. A quote from the Linux PAM S.A. Guide: "It is the purpose of the Linux-PAM project to separate the development of privilege granting software from the development of secure and appropriate authentication schemes. This is accomplished by providing a library of functions that an application may use to request that a user be authenticated."

The Authen-PAM module at CPAN will help.