The present study aimed to identify the subclinical infection and tissue-specific localization of foot-and-mouth disease (FMD) virus RNA and/or antigen in Asiatic-buffaloes as their possible involvement in starting new outbreaks is still up for debate. Serum, oropharyngeal fluid (OPF), and 11 distinct tissue-samples were taken from the slaughterhouses from Asiatic-buffaloes (n = 70) and processed for 3AB3-non-structural protein (NSP) antibody titre estimation, virus isolation and genome detection, haematoxylin and eosin (HE) examinations, and indirect immunofluorescence assays, respectively. Of these, it was found that 04 (serum), 14 (OPF), and 18 (tissue) samples tested positive for NSP Ab, and FMD Viral genomic RNA/Ag, respectively. Nevertheless, FMD Virus (FMDV) could not be isolated from any of the positive OPF or tissue samples; this might be because of limited sensitivity of the test system/low concentration of FMDV. The dorsal-soft-palate (DSP)-2 was shown to have the highest rate of FMDV detection by immunofluorescence microscopy, followed by DSP1, dorsal nasopharynx (DNP)-2, DNP1, and palatine tonsil (PTON). Therefore, in asymptomatic Asiatic-buffaloes living in natural environments, DSP and DNP might be the primary FMDV localization sites. However, since it can be difficult to distinguish between temporally acute subclinical infections and persistent infections in the field, particularly in abattoir surveillance, the site of viral RNA/antigen localization needs to be confirmed with known persistently infected buffaloes under controlled conditions. Moreover, there was no evidence linking the 3AB3 NSP antibody positive rate to the genome identification in tissue samples and OPF. To determine whether a correlation occurs at all, more samples must be assessed using various procedures and tests.