A more complete answer would be it is not possible with ftp(at least the ftp program installed on centos 6).
Since you wanted an un-attended process, "pts"'s answer will work fine.
Do the unattended upload with curl instead of ftp:
curl -u user:password -T file ftp://server/dir/file
%40 doesn't appear to work.
[~]# ftp domain.com
ftp: connect: Connection refused
ftp> quit
[~]# ftp some_user%40domain.com@domain.com
ftp: some_user%40domain.com@domain.com: Name or service not known
ftp> quit
All I've got is to open the ftp program and use the domain and enter the user when asked. Usually, a password is required anyway, so the interactive nature probably isn't problematic.
[~]# ftp domain.com
Connected to domain.com (173.254.13.235).
220---------- Welcome to Pure-FTPd [privsep] [TLS] ----------
220-You are user number 2 of 1000 allowed.
220-Local time is now 02:47. Server port: 21.
220-This is a private system - No anonymous login
220-IPv6 connections are also welcome on this server.
220 You will be disconnected after 15 minutes of inactivity.
Name (domain.com:user): some_user@domain.com
331 User some_user@domain.com OK. Password required
Password:
230 OK. Current restricted directory is /
Remote system type is UNIX.
Using binary mode to transfer files.