Codeigniter duplicate content with mod_rewrite

In codeigniter, once you enable short urls, you have the possibility of duplicate content because although your new URLs look like:

http://domain.com/privacy_policy

You can still manually access the old links, which still load when you type in:

http://domain.com/index.php/privacy_policy

My htaccess file, per the manual, looks like:

RewriteEngine On
RewriteBase /

RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ /index.php/$1 [L]

What should I do to solve this problem?

You could resolve this issue by redirecting the user agents to a new URL.

Method #1: Using htaccess

Use the following just after RewriteBase /, as the first RewriteRule:

RewriteCond %{THE_REQUEST} index\.php
RewriteRule ^index.php(?:/(.*))?$ $1 [R=301,L]

You might want to change $1 to http://example.com/$1 if you haven't used RewriteBase.

The other rules MUST come after the above rule.

Method #2: Handle with PHP

I'd suggest to extend the CI_Controller as follows:

class MY_Controller extends CI_Controller
{
    public function __construct()
    {
        // Execute CI_Controller Constructor
        parent::__construct();

        // Get the index page filename from config.php
        // For perior to PHP 5.3 use the old syntax.
        $index = index_page() ?: 'index.php';

        // Whether the 'index.php' exists in the URI
        if (FALSE !== strpos($this->input->server('REQUEST_URI', TRUE), $index))
        {
            // Redirect to the new address
            // Use 301 for permanent redirection (useful for search engines)
            redirect($this->uri->uri_string(), 'location'/*, 301*/);
        }
    }
}

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However, the search engines won't index the URLs which look like index.php/privacy_policy, Unless you've used such URL addresses in your page.

Also, you could use a canonical link element within your pages to make search engines index only one version of the page for their search results:

<link rel="canonical" href="http://domain.com/privacy_policy">

Particularly in CodeIgniter:

<link rel="canonical" href="<?php echo base_url(uri_string()); ?>">