If you are running ws-ftp it's pretty easy, just add the following line to your /etc/ftpaccess file:
shutdown /etc/shutmsg
You can create the /etc/shutmsg file with a custom message in it to suit you.
Else, as crowe said, either comment the port out in the /etc/services file, ot comment the process out in the /inetd.conf file. This will require a SIGHUP of the inetd process to make effective.