Right now, this vaccine is distributed under an EU-wide “Conditional Marketing Authorisation” based on a recommendation from the European Medicines Agency. This authorisation constrains what can be done with the vaccine, certainly as far as the manufacturer, marketing authorisation holder, and national governements are concerned (legally, individual practitioners might have some leeway in how they administer a medicine). Similar processes exist elsewhere.
Under existing European law, neither national governments nor even the EU Commission itself are supposed to circumvent this process and allow random compounds to be used as medicinal products or issue arbitrary recommendations for their use without consulting the agencies they set up to regulate this. From that perspective, unless it wants to issue another authorisation, the Czech government cannot unilaterally do anything.
EU law does however foresee other types of approvals for medicinal products that could be issued at the national level:
- Emergency Use Authorisation
- National/Mutual Recognition Procedure
Legally, the Czech Republic could issue an Emergency Use Authorisation for a Covid-19 vaccine without asking the EU for permission but all EU countries indicated earlier this year that they preferred to follow the regular “Conditional Marketing Authorization” process. Consequently, I assume that no manufacturer applied for approval at the national level.
In many cases, manufacturers can also apply for approval through a National/Mutual Recognition Procedure but EU law restricts those. In particular, the centralised procedure is mandatory for products developed with certain techniques like recombinant DNA technology. If I understand the Pfizer/BioNTec vaccine correctly, this rule seems to preclude a national marketing authorisation for that particular product (but that will not necessarily be the case for all other vaccines).
In both cases, the approval would not be solely in the hands of the Czech cabinet but should be initiated by an application by the manufacturer and go through the National Competent Authority, namely the State Institute for Drug Control. That, rather than EU harmonization, is what ties the hands of the Czech government.