/etc/apache2/conf-available/nagios3.conf is in nagios3-cgi 3.5.1.dfsg-2.1ubuntu1.
This file is owned by root:root, with mode 0o777.
It is a symlink to /etc/apache2/conf-available/../../nagios3/apache2.conf
/etc/apache2/conf-available/../../nagios3/apache2.conf