Long-term transport or storage of fruits is often shadowed by severe degradation of fruit quality. Therefore, two popular apple cultivars produced in Nagano prefecture, Japan, were studied for quality variation during refrigerated container (reefer container) storage, followed by a sensory evaluation for some of the flavor components. The evaluation of the green color cultivar, 'Ohrin' and red color cultivar 'Sun Fuji' apple was done with the aim of reducing the quality loss during storage and to understand its effect on sensory qualities. Three different reefer containers; i) a standard refrigerator container, ii) a container which provides an electric field inside, and iii) a container integrated with ethylene and aldehyde absorbent made of charcoal and catechin were evaluated for the fruit quality during three weeks of storage within three- to four-day intervals. As quality parameters, fresh weight loss, surface color measured by three aspects L (lightness), a (red/green) and b (yellow/blue), total soluble solids content measured by degrees Brix index and firmness were evaluated. After the storage, a questionnaire survey was conducted for the flavor components. Preservation of color quality in 'Ohrin', was significantly higher in reefer 2 and for 'Sun Fuji' reefer 3 was higher. Fruits in reefer container 3 had higher firmness for 'Ohrin', and reefer 2 resulted in lower Brix values. Sensory evaluation showed higher preference for both apple cultivars stored in reefer 3, concluding it had much higher quality preservation by reducing the ethylene effect.