Country report: ECDC Public Health Emergency Preparedness Assessment for the Czech Republic, 2026

Background

This report presents the findings and recommendations of the first assessment conducted in the Czech Republic. This involved a desk review of relevant documents, followed by a five-day country visit that took place during the period 16−20 February 2026. As per the assessment methodology, all of the 16 capacities included in Article 7 of the Implementing Regulation (EU) 2023/1808 self-assessment template were assessed, with five of them considered in-depth: Laboratory (Capacity 3); Surveillance (Capacity 4); Health Emergency Management (Capacity 6); Antimicrobial resistance (AMR) and healthcare-associated infections (Capacity 12) and Zoonotic diseases and threats of environmental origin (Capacity 10). 

Key findings

The Czech Republic is administratively divided into 13 regions and the capital city of Prague, with the regions comprising 76 districts. The public health system in the Czech Republic is decentralised, with the Ministry of Health holding a central governing role at the national level, ensuring coordination across the regions and with the European Union level, and the National Institute of Public Health (SZÚ) having a technical advisory role. The Ministry of Health recently established an Emergency Operation Centre (EOC) within its organisational structure. The country has a decentralised system of 14 Regional Public Health Authorities (KHS) and two Health Institutes (ZÚ) with a degree of autonomy. National Reference Laboratories are located at the SZÚ and ZÚ, providing coordination and support for the public health laboratories in the country. 

The provision of health services and a substantial part of the operational responsibility for preparedness and response to emergencies is placed at the regional level, with central coordination in certain cases. The Ministry of Interior and regional fire rescue services are the main coordination bodies for civilian crises. Outbreak investigation is conducted at regional and local level; the Ministry of Health only coordinates at national level during outbreaks affecting more than one region, or international outbreaks. The involvement of SZÚ in outbreak investigations depends on whether local public health authorities and clinical and public health laboratories have requested methodological and specialised support. 

A key strength of the country is a comprehensive legislative framework that guides and governs surveillance and laboratory activities, as well as preparedness and response to emergencies. Two acts that constitute the backbone of public health emergency preparedness and response are the Protection of Public Health Act No. 258/2000 Coll. and the Crisis Management Act No. 240/2000 Coll., with additional legislative instruments complementing the overall framework. The country has many topic-specific plans at all administrative levels for preparedness and response to all-hazard emergencies with an impact on human health. 

The public health system is evolving to address new needs and emerging risks. A revision of the national risk profiling is currently underway, reflecting a proactive approach to identifying and prioritising threats, including those to public health. However, risk assessment of public health threats is conducted on an ad-hoc basis and a risk assessment methodology at the national level is not in place. The country also plans to develop a generic, all hazard prevention, preparedness and response plan (PPR), embedding the One Health approach.  

Significant progress is also being made with digitalisation, and an integrated and automated surveillance system based on electronic health records is being rolled out.  Indicator-based surveillance of antimicrobial resistance (AMR) and healthcare-associated infections (HAIs) is established at the local and, for some indicators, national level, demonstrating efforts to address these critical public health challenges. However, further work is needed, including the strengthening of surveillance and approval, funding and implementation of the national action plan (NAP) on AMR. Across all areas, resource limitations – both human and financial – were identified as critical constraints at both regional and national level. Recruitment and retention of technical staff were reported to be a significant challenge. These limitations inevitably hinder more ambitious public health prevention, preparedness and response goals. It is essential to address these resource gaps in order to maintain the country capacity to prevent and respond to health emergencies and to further implement the ongoing reforms of the public health system.