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SSH keys should be in the home dir for nagios, which is typically /var/spool/nagios/.ssh and owned by nagios:
mkdir /var/spool/nagios/.ssh ssh-keygen -f /var/spool/nagios/.ssh/id_rsa chown nagios:nagios /var/spool/nagios/.ssh -R
Remotely install the agent on localhost:
cat /var/spool/nagios/.ssh/id_rsa.pub >> /root/.ssh/authorized_keys
If it works, you should see something like this: