Genetic background, environmental conditions, and agronomical practices could influence yield components, grain quality, and physicochemical properties of rice. The study aim was to investigate the variations in yield potential, quality traits, and morphological observation among Akitakomachi (japonica), IR-28 (indica), and NERICA-4 (hybrid) varieties under the same environmental and agronomical conditions. For this, the cultivars were compared in a randomized complete block design with three replications at the paddy field of Tsukuba International Center, JICA, Tsukuba, Japan in 2017. All cultivars were transplanted at a spacing of 15×30 cm using three seedlings per hill. The results exhibited that Akitakomachi had a higher number of panicles per m2 (344.3), and the ripening ratio (94.3%) across all cultivars. In addition, IR-28 and Akitakomachi achieved significantly higher rough rice yield (6.9 t/h & 6.1 t/h), respectively, compared to NERICA-4 (4.9 t/h). However, NERICA-4 was associated with the significantly higher amylose and protein contents, which resulted in the reduction of the taste point than other cultivars. Furthermore, the lowest grain transparent (34.2%) and highest chalky grain (47.7%) were obtained in NERICA-4, which leads to lower grain quality. IR-28 and NERICA-4 were classified as long and slender grain types, whereas, Akitakomachi as a short and medium grain, respectively. The micrographs observation displayed that regular starch granules with polyhedral shape were arranged without air gaps in transparent grains of all cultivars. In contrast, the endosperm of chalky grains in NERICA-4 and IR-28 revealed that irregular starch granules with round shape were loosely packed. Thus, each cultivar should be considered based on growing regions and the cultivated aims.