By default it’s alias: you-domain.com/nagios3 and to do it as standalone site follow below instruction…

• a2disconf nagios3
• ln -s /etc/nagios3/apache2.conf /etc/apache2/sites-enabled/your-domain.com.conf
• modify this file to look like:

  <VirtualHost *:80>
          ServerAdmin webmaster@example.com
          ServerName nagios.example.com
  
          ScriptAlias /cgi-bin/nagios3 /usr/lib/cgi-bin/nagios3/
  
          Alias /stylesheets /etc/nagios3/stylesheets/
          Alias / /usr/share/nagios3/htdocs/
  
          DocumentRoot /usr/share/nagios3/htdocs/
  
          <DirectoryMatch (/usr/share/nagios3/htdocs|/usr/lib/cgi-bin/nagios3|/etc/nagios3/stylesheets)>
                  Options FollowSymLinks
  
                  DirectoryIndex index.php index.html
  
                  AllowOverride AuthConfig
                  Order Allow,Deny
                  Allow From All
  
                  AuthName "Nagios Access"
                  AuthType Basic
                  AuthUserFile /path/to/nagios3/htpasswd.users
                  require valid-user
          </DirectoryMatch>
  
          <Directory /usr/share/nagios3/htdocs>
                  Options +ExecCGI
          </Directory>
  
          ErrorLog ${APACHE_LOG_DIR}/nagios.example.com-error.log
          LogLevel warn
          CustomLog ${APACHE_LOG_DIR}/nagios.example.com-access.log combined
  </VirtualHost>
  

• in file /etc/nagios3/cgi.cfg change url_html_path from /nagios3 to /
• service apache2 restart