According to the Medicinal Products Licensing Ordinance (MPLO), the requirements as per EU GMP and the GMP guidelines of PIC/S are both valid in Switzerland. The Swiss Institute for Therapeutic Products ("Swissmedic") has now published a short statement on how to handle differences between the different GMP guidelines.
Generally, the compliance with both sets of guidelines is expected; in cases of discrepancies between the guidelines, the more stringent requirement applies. While the requirements are the same in most cases, they are not completely identical. Since a general harmonisation between both regulations is pursued, however, it has so far been accepted if the requirements of the PIC/S GMP guideline only were met for a short period of time until the requirements of the other guideline were added or updated. This practice, which had so far been tolerated, is now no longer accepted. The reason therefore is that the EU GMP guidelines usually enter into force earlier than the ones of PIC/S GMP. As an example, Swissmedic names the requirement to avoid cross contamination in the EU GMP Guideline, which has not been added to the PIC/S guidelines, yet.
Please also see the original announcement entitled "Procedure for discrepancies between EU and PIC/S GMP".