For logistical purposes Amazon is using 7 warehouses throughout Europe, and even more new warehouses are expected to be opened. Amazon Pan-EU Program currently includes the United Kingdom, Germany, Italy, France, Spain, Czech and Poland. 

If you are joining the Pan-EU program you will start using the listed Amazon warehouses. According to the current EU legislation if you sell a product from a warehouse you must have VAT registration and apply local VAT from the very first euro.

Therefore, you need to have VAT registration in the countries where you use the warehouse and submit the VAT returns in all the Pan-EU FBA countries.