There are many ways of setting the fully qualified domain name on a Linux machine. Some set it directly in /etc/hostname, something which, after reboot, will make the hostname command return the fqdn:

# hostname
host.example.com

This is a bit of the easy and quick fix, and will not necessarily work with all systems. Also, it doesn’t work to well on multi-domain systems.

A better trick that I found while dealing with Openstack hosts that are managed via cloud-init is to set just the hostname in /etc/hostname, then add an entry to /etc/hosts. It doesn’t have to be an entry that points at any real IP address, just as it contains both the FQDN and the hostname. So:

# cat /etc/hosts
127.0.1.1  hostname.example.com hostname

# cat /etc/hostname
hostname

This is something I have been struggling with for years, yet the fix is so easy.