The EU Commission has reminded all EU states on its website that “it is the responsibility of the Member States to refuse entry on public health grounds to individual 3rd country nationals” where they are judged to be a risk to public health. This applies at all borders between an EU member and third country.
It wants the external border of the EU to be reinforced, with migrants kept separate on arrival until their health has been checked.
It has also made clear it does not recommend that action at internal borders within the EU between member states. It states
“It should also be noted that according to the WHO and others, reintroduction of border controls at internal borders in order to refuse entry is not considered an appropriate preventive (or remedial) measure”