I got this error when I verified my configuration but when I check the path of the main configuration file(/usr/local/nagios/etc/nagios.cfg) it was there.
$ /usr/local/nagios/bin/nagios -v ../etc/nagios.cfg
Copyright (c) 1999-2007 Ethan Galstad (nagios.org)
Last Modified: 03-08-2007
Reading configuration data...
Error in configuration file '/usr/local/nagios/etc/../etc/cgi.cfg' - Line 16 (UNKNOWN VARIABLE)
***> The name of the main configuration file looks suspicious...
Make sure you are specifying the name of the MAIN configuration file on
the command line and not the name of another configuration file. The
main configuration file is typically '/usr/local/nagios/etc/nagios.cfg'
***> One or more problems was encountered while processing the config files...
Check your configuration file(s) to ensure that they contain valid
directives and data defintions. If you are upgrading from a previous
version of Nagios, you should be aware that some variables/definitions
may have been removed or modified in this version. Make sure to read
the HTML documentation regarding the config files, as well as the
'Whats New' section to find out what has changed