First of all, you shouldn't be using Excel as a data store for your website. But if you have no other choice...
I'm guessing that you have a web application that manipulates the Excel file. What you can do is place the Excel file outside of the publicly accessible path. For example, if your public website is hosted at /var/www/myapp/public, and the public
directory is accessible to the outside world, then you could place the Excel file in /var/www/myapp and make sure that that directory isn't served to the outside world by the web server. Your application should still be able to access the file.