Yes. You can use the invoice discount function for this. Here you can even use it to specify a min. amount to avoid the fee.
The Invoice Discount Code on the Customer to specify different levels.
Not sure why Mohana suggested that link.
Since it's version 2013 R2, then he gave the "correct" answer in his own blog:In NAV 2013 R2, this is standard setup, no need for code.