This is a fairly common problem and John Conde's suggestion to use canonical URL's is a safe bet.
You may have other options, depending upon how comfortable you are with editing your server configuration and PHP scripts.
Apache mod_rewrite directive
Advantages: Does not require modifying your PHP application.
Disadvantages: Processing overhead for the rewrite engine on every request. (Note that the disk access overhead associated with enabling the
AllowOverride directive for
.htaccess support is typically greater than the modest processing overhead incurred by mod_rewrite)
The following mod_rewrite directives will permanently redirect users to the directory requested if
index.php is appended:
RewriteRule (.*)\/index\.php$ /$1/ [R=301,L]
Advantages: Does not require use of mod_rewrite, processing overhead incurred only on PHP file requests.
Disadvantages: Requires editing PHP scripts and introduces potential for scripting errors. Requires knowledge of PHP troubleshooting should errors occur.
If your application consists of multiple files which all include the same heading file or template, you can add the following conditional block to the file before any HTML is printed or echoed: (calls to PHP's header() function will fail if any output has been sent to the user)
$uri = strtok($_SERVER['REQUEST_URI'],'?');
if ( 'index.php' == substr($uri, -9) )
$redirect_uri = ($_SERVER['HTTPS']) ? 'https://' : 'http://';
$redirect_uri .= $_SERVER['HTTP_HOST'];
$redirect_uri .= substr( $uri, 0, strlen($uri) - 9 );
header( 'HTTP/1.1 301 Moved Permanently' );
header( 'Location: ' . $redirect_uri );