Look at http://www.ford-hutchinson.com/~fh-1-pfh/ftps-ext.html for lots of info on FTP-SSL. It has a list of clients that support SSL, includng command-line clients that could be run from Perl.

Also, you might want to investigate if FTP is the right solution. HTTPS is much simpler and better supported. It isn't ideal for transferring files it can be used for that. SSH and SFTP are also good for transferring and manipulating files securely.