The beginnings of the National Laboratory for Health, Environment and Food date back to 1922, when a Permanent Bacteriological Station in Ljubljana was established for the former Carniola territory, by a decree of the Ministry of National Health in Ljubljana.

The following year, a Permanent Bacteriological Station was established in Celje for the territory of the former Styria and Prekmurje region. In the same year, 1923, the Ministry of National Health in Belgrade determined that the new institute will be called the Hygiene Institute in Ljubljana. 

In 1924, a department for disinfection and disinsection was established at the Institute of Hygiene.

A year later, the Hygiene Institute and the Permanent Bacteriological Station in Ljubljana were merged into a single Hygiene Institute with three departments: The Bacteriological-Serological Department, the Water and Food Research Department, and the Hygiene-Propaganda-Didactic Department.

After the Second World War, the Institute of Hygiene was divided into the Bacteriological and Epidemiological Institute, and the Central Food Laboratory. 

In 1951, the government of the People’s Republic of Slovenia established the Central Hygiene Institute (CHZ), which became the highest national expert institution for the hygiene service.

Ten years later, in 1961, after the adoption of the Health Care and the Organisation of Health Care Act by the Assembly of the Socialist Republic of Slovenia, the CHZ was reorganised and renamed the Institute of Health Care (ZZV), which performed socio-medical, hygienic, and epidemiological activities.

On the basis of the Health Care Activity Act, the independent Slovenian state established the Institute of Public Health (IVZ) for the territory of the Republic of Slovenia in 1992, as well as regional health care institutes for the area of multiple municipalities: Maribor, Murska Sobota, Celje, Novo mesto, Koper, Nova Gorica, Ljubljana, Kranj, Ravne na Koroškem. 

In 2013, based on the amendments to the Health Care Act, the Government of the Republic of Slovenia adopted the Decision on the Establishment of the National Institute of Public Health (NIJZ), and the Decision on the Establishment of the National Laboratory for Health, Environment and Food (NLZOH).

The National Laboratory of Health, Environment and Food started to operate in 2014.