Open file “application\helpers\MY_url_helper.php”, lines 82 and 83. There is transition, for croatian example but you can also add yours:
array('č','ć','ž','š','đ', 'Č','Ć','Ž','Š','Đ') => array('c','c','z','s','d', 'c','c','z','s','d')
You can also enable non-standard characters in uri, hints: