Php has more extension than the customary ‘.php’.
If you are using for some reason the extension other than php, then you have to let Mr Apache that you intend to treat .phtml just like that of php files.
You can accomplish this using a simple .htaccess file that sits on the root folder of your website.
AddHandler application/x-httpd-php .php .php3 .php4 .php5 .phtml .html .htm
Yup that should take care of the mess.