Background The tubarial glands (TGs) are recently reported as newly found salivary gland structures that can be organs at risk predominantly localized in the tori tubarius in the nasopharynx using prostate-specific membrane antigen positron emission tomography/computed tomography (PSMA PET/CT). The aims of this study were to analyze uptake in the TGs compared with that in the other salivary glands and palatine tonsils using 99mTc-pertechnetate SPECT/CT, 18F-FDG PET/CT, and 11C-methionine PET/CT, and to confirm whether these three imaging modalities are useful in evaluating the physiological function of the TGs. Twelve and 130 patients, who underwent 99mTc-pertechnetate SPECT/CT and 18F-FDG/11C-methionine PET/CT, respectively, were retrospectively included. 99mTc-pertechnetate uptake in the tori tubarius was visually assessed and semiquantitatively compared with that in the background, parotid salivary glands (PSGs), submandibular salivary glands (SmSGs), and sublingual salivary glands (SlSGs). Correlations of 18F-FDG and 11C-methionine uptakes in the tori tubarius with those in the other three salivary glands and palatine tonsils were analyzed. Results 99mTc-pertechnetate uptake in the tori tubarius was invisible and was not significantly higher than that in the background. Both 18F-FDG and 11C-methionine uptakes in the tori tubarius were correlated with that in the palatine tonsils (r = 0.56, p < 0.0001; r = 0.48, p < 0.0001, respectively). 18F-FDG uptake in the tori tubarius was not positively correlated with that in the PSGs, SmSGs, and SlSGs (r = –0.19, p = 0.03; r = –0.02, p = 0.81; r = 0.12, p = 0.17, respectively). 11C-methionine uptake in the tori tubarius was correlated with that in the SmSGs and SlSGs (r = 0.24, p = 0.01; r = 0.32, p < 0.01, respectively), but not with that in the PSGs (r = 0.16, p = 0.08). Conclusions The TGs were undetectable on 99mTc-pertechnetate SPECT/CT. Both 18F-FDG and 11C-methionine uptakes in the tori tubarius were clearly affected by that in the palatine tonsils and was little related to that in the other salivary glands. Therefore, it seems difficult to evaluate the physiological function of the TGs as salivary glands using 99mTc-pertechnetate SPECT/CT, 18F-FDG PET/CT, and 11C-methionine PET/CT imaging.