Pursuant to §27 of the German Animal Health Act (TierGesG) the Friedrich-Loeffler-Institut acts as National Reference Laboratory (NRL) for more than 70 notifiable and reportable animal diseases. The reference laboratories have been accredited by the Deutsche Akkreditierungsstelle GmbH (DAkkS) according to ISO/IEC 17025. They clarify suspected cases, provide advice to the veterinary authorities and conduct ring trials or carry out similar quality assurance measures for animal disease diagnostics in Germany. Within the frame of this activity, the FLI publishes a collection of official sampling and investigation procedures for notifiable animal diseases and the Annual Animal Health Report.
On the international level, the FLI has been designated as "Collaborating Centre for Zoonoses in Europe" of the World Organisation for Animal Health (OIE). Furthermore, it houses OIE reference laboratories for avian influenza, Newcastle disease, bovine herpesvirus-1 infection, brucellosis, chlamydiosis, glanders, and rabies.
A “Collaborating Centre for Rabies Surveillance and Research” of the World Health Organization (WHO) is also located at the FLI.
The Food and Agriculture Organization of the United Nations (FAO) has designated the FLI as Reference Centre for Influenza in Animals, Newcastle Disease of Poultry and Classical Swine Fever.