Включить модуль перезаписи URL в Apache2:
a2enmod rewrite
Изменить /config/config.php
$config['index_page'] = "index.php";
до
$config['index_page'] = "";
А также
$config['uri_protocol'] = 'AUTO';
до
$config['uri_protocol'] = 'REQUEST_URI';
Правильный путь .htaccess:
#AddHandler application/x-httpd-php5 .php
<IfModule mod_rewrite.c>
RewriteEngine On
#RewriteBase /
#Removes access to the system folder by users.
#Additionally this will allow you to create a System.php controller,
#previously this would not have been possible.
#'system' can be replaced if you have renamed your system folder.
RewriteCond %{REQUEST_URI} ^system.*
RewriteRule ^(.*)$ index.php?/$1 [L]
#Checks to see if the user is attempting to access a valid file,
#such as an image or css document, if this isn't true it sends the
#request to index.php
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?/$1 [L]
</IfModule>
<IfModule !mod_rewrite.c>
# If we don't have mod_rewrite installed, all 404's
# can be sent to index.php, and everything works as normal.
# Submitted by: ElliotHaughin
ErrorDocument 404 index.php
</IfModule>
php_flag short_open_tag on
<FilesMatch "\.(php)$">
FileETag None
<IfModule mod_headers.c>
Header unset ETag
Header set Cache-Control "max-age=0, no-cache, no-store, must-revalidate"
Header set Pragma "no-cache"
Header set Expires "Wed, 11 Jan 1984 05:00:00 GMT"
</IfModule>
</FilesMatch>
Перезапустите службу Apache2:
sudo systemctl restart apache2.service
Надеюсь, это поможет.