On 1 January 1992 the Institute was reinstated as a centralised institution with a nationwide sphere of influence and a mission to protect and promote public health, engage in prevention of disease and monitor the impact of the environment on population health. Apart from the main centres and departments, the NIPH contained seven WHO collaborating centres and 51 national reference centres and laboratories during 1992 – 1994. The Institute became the headquarters of the system for monitoring the impact of environment on population health. It was also closely engaged in educational activities at the 3rd Medical Faculty of Charles University and post-graduate education in preventive medicine. Doc. Jaroslav Kříž became the director of the NIPH on 1 May 1994.

During the 1990s', the NIPH successfully revived the tradition of scientific research, coping with over 100 research projects (financed from both home and abroad), increased the output of published work by its specialists and incepted a project aimed at analysis of infectious, environmental and behavioural health hazards and their prevention. A new activity is health education, organised by the institute since 1996 after the abolishment of the National Health Promotion Centre. The NIPH managed the National Health Promotion Programme and prepared a national variant of the WHO 'Health for All' project.

The NIPH played an important role in other nationwide preventive programmes, for instance the Action plan for health and environment in the Czech Republic, The national programme for prevention of AIDS and coordination of the prevention of iodine deficit. The Institute has been actively engaged in pre- and post-graduate education and has provided a great deal of consultation assistance to field researchers. It has prompted the development of new projects such as the programme for external quality assessment and inter-laboratory test comparisons.

At the beginning of 2001, Doc. J. Kříž asked be relieved of his duties as a director and was succeeded on 1 July 2001 by the Chief Public Health Officer of the Czech Republic, Dr Michael Vít, PhD.

At the end of the same year, the Centre for Healthcare Quality was established at the NIPH on the request of the Minister of Health Prof. B. Fisher. This centre is engaged in evaluating the quality of healthcare in preventive and clinical medicine.

Dr Jaroslav Volf, PhD was named head of the Institute on 1 January 2003. Simultaneously, as stipulated by par. 86 of law no. 258/2000, in the wording of law no. 320/2002, the National Institute of Public Health has been designated a contributory organisation. However, new director, official status and legal backing were not the only changes that influenced the role of the NIPH within the public health system of the Czech Republic.