Lots of options other than CGI directly. You could use ftp, sftp, scp, ssh protected ftp, rsync, wget. You could use server pull rather than client push, letting the remote server pull the file from your local box. You could just do it with sockets. There are lots of ways to transfer files.

Assuming that this is a regular upload you could just put the data into a browsable location locally (assuming you have a web server onsite), protect it with a .htaccess file and just set a cron job to get it whenever it suits using wget.