Mutations in the starch synthesizing genes of cereal crops with altered starch properties has been utilized to widen the applications of grain, flour and starch. Here, rice spontaneous mutants that lacked starch branching enzyme 1 (BEI) activity were identified from among local upland rice cultivars. Two cultivars, Kurnai and Hiderishirazu-D, lacked BEI activity in the developing endosperm, and their reserved starch was rich in short chains of amylopectin and showed a low pasting temperature (PT) of rice flour. These features are similar to those of the induced starch branching enzyme 1 gene (Sbe1) mutant of rice. We detected polymorphisms in the Sbe1 of the Kurnai and Hiderishirazu-D cultivars and used them to develop PCR markers suitable for selecting breeding lines and cultivars with BEI deficiency. We assessed the possible utilization of BEI deficiency in waxy rice processing with the use of both the spontaneous and induced BEI-deficient lines. Rice cakes made from BEI-deficient lines maintained their softness for longer periods than those made from functional BEI lines. Our results suggest that use of BEI-deficient waxy rice could improve the quality and extend the shelf life of waxy rice products.