Here we examined the properties of endosperm starches and the physical properties of cooked rice from four cultivars of Japanese upland rice containing M-type amylopectin (Chikanarijyun1, Kairyo13, Mogamichikanari1 and Hokkaiakage); S-type Nipponbare and L-type Kasalath served as standards. The amylopectin chain ratio (ACR ; ratio of the short chains of DP ≤ 10 to the short and intermediate chains of DP ≤ 24) of M-type amylopectin was higher than L-type amylopectin, and lower than S-type amylopectin. The degree of disintegration of rice grains in 5 M urea solution was in the order Nipponbare > M-type amylopectin > Kasalath. Specifically, the disintegration score of rice grains decreased as the ACR decreased. The apparent amylose (AAM) contents were in the order Kasalath > M-type amylopectin, except Kairyo13 > Nipponbare > Kairyo13. These results indicated that there was no relationship between the AAM contents and ACR. The hardness of freshly cooked and stale rice was in the order Kasalath > M-type amylopectin > Nipponbare. The stickiness of freshly cooked rice was in the order Nipponbare > Kairyo13 > M-type amylopectin, except Kairyo13 > Kasalath and that of stale rice was in the order Nipponbare > M-type amylopectin > Kasalath. The stickiness of freshly cooked rice of Kairyo13 was the highest in the M-type amylopectin cultivars, because it had the lowest AAM content in all cultivars. Freshly cooked rice of Kairyo13 was harder and less sticky compared with that of Nipponbare. It was possible that the ACR of Kairyo13 was lower than that of Nipponbare.