Can you describe how you are creating the ssh session between the Nagios Xi server and the Ubuntu server?
Are you using the nagios user account for the ssh session while logged in to the Xi server as the nagios user?
Can you run the following check_by_ssh command from the XI server while logged in as the nagios user and post back the output?
ls -al /home/
ls -al /home/nagios/
ls -al /home/nagios/.ssh
Also, are all of your service checks failing that are over SSH or are you just attempting to use the check_disk one? I'm wondering if the problem is under check_disk specifically as there seems to be a bug on the Ubuntu forums with something similar. https://bugs.launchpad.net/ubuntu/+sour ... ug/1516451
To add to what @tgriep mentioned - Is check_disk the only one that you are using with check_by_ssh?