The National Japanese Encephalitis Laboratory, designated and recognized by the WHO in March 2009, is hosted by the RITM-Department of Virology National Reference Laboratory for Dengue and Other Arboviruses.

The National Japanese Encephalitis laboratory follows the standard procedures for JE serological investigation using Panbio JE/Dengue IgM Combo ELISA (Alere, Australia) as recommended by WHO. The JE laboratory is reviewed annually by the WHO Western Pacific Regional Office based on laboratory performance (confirmatory testing, proficiency panel testing, and accreditation visits). The laboratory has been fully accredited by the WHO in 2010 up to the present.

The National JE Laboratory continues to receive samples for JE diagnosis, to include cases referrals from clinicians for patient diagnosis and management, as well as from the Acute Encephalitis Syndrome (AES) surveillance of the DOH National Epidemiology Center.