For a short-term stay on the basis of a bilateral agreement, data is recorded in the Entry/Exit System (EES) by the Foreign Police Service only if foreigner is present in person.
If you enter the territory of Czechia on the basis of a bilateral agreement, you may ask a Foreign Police Service officer during border control to indicate the fact that you will stay in Czechia on the basis of a bilateral agreement. The record will be made by the Foreign Police Service inspectorate at the international airport.
If you are already in the territory on the basis of visa-free travel and subsequently plan to continue staying in Czechia on the basis of a bilateral agreement, you must come in person to the locally competent office of the Foreign Police Service, where a Foreign Police Service officer will make a record in the EES if you meet the conditions for staying in the Czechia on the basis of this agreement.
Questions regarding the indication of short-term stay on the basis of a visa-free bilateral agreement may be addressed to the Department of the Foreign Police Service. You can also find the list of locally competent offices here.