Question

I am using apache server.
Is there a way to prevent users from accessing my include files directly ?
But only allow the server the access to those ?

Answer 1

Another way is to have the include files outside of the directory the site is served from. For example:

/
    includes/somefile.php
    http/index.php

So the Web site is served from http/, but includes are outside of that directory, meaning no one can access them directly from a Web browser, but your scripts can include them like this:

<?php
require_once '../includes/somefile.php';
[...]