Hmm...I had not thought of that. The situation would be the same if you used an SMB server instead of FTP. I suspect an anonymous account is out of the question?
I've never done this myself, but looking at the man page for apt-get shows that two configuration files can be used:
/etc/apt/apt.conf
/etc/apt/preferences
Although my system does not have these.
Also a quick Internet search brought this up:
http://www.debian-administration.org/articles/177
At the bottom of this page it shows how to include login and password in a file that is under /etc/apt/apt.conf.d/
Sorry I could not be more helpful.
Regards,
OPC