Transferring stock within the same company but different VAT numbers

You will need to set both sites up as Customers, and both as Suppliers, then use Purchase Order-Customer Order transactions to sell intersite.  You can turn on the automated intersite process if you want to automate the creation of the CO in the supply site and even up to the creation of the invoice from the supply site to the demand site.

@ShawnBerk , how can we create invoice for inter-site transactions where both the site belong to same company??

Regards-

Nahin

You could look at using Distribution Orders.