It's possible to script ftp commands using the 'expect' scripting language. You would then add your script to a cron job to have it run on a regular basis.
http://linux.die.net/man/1/expect
But this it's considered extremely bad security policy to hard code usernames and passwords in a script. Rsync should be used. You really need to get your admin to disable ftp and enable ssh as soon as possible.