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While the recent emergence of gene editing technologies has attracted wide attention from scientists, we have scarce empirical evidence concerning consumer attitudes toward application of such technologies on agricultural products. We quantitatively investigated this topic by utilizing two web-based surveys conducted in December 2016 to February 2017. The first survey used 3,000 samples from a large opt-in panel of online population in Japan. For the second survey, we adopted opportunistic sampling through academic societies’ websites and mailing lists, and recruited 197 researchers both who have expertise in molecular biology along with researchers who have other fields of specialty. With those data, we statistically compared the level of peoples’risk / benefit perceptions for applying different technologies on agricultural products, i.e., attitudes toward conventional breeding, genetic modification, and gene editing, using repeated measure analysis of variance. Further, we examined how the expertise or scientific literacy influences those perceptions by contrasting the statistical results between researchers and lay publics. The results showed that people tended to have a more favorable attitude toward gene editing than genetic modification. Such improvements were however only a few extents among the lay publics or non-microbiology researchers, compared to conventional breeding. Trends in Experts' responses were significantly different from other two groups. Based on those empirical evidences, we discuss theoretical and practical implications for Agri-food STS and risk communication. Although the study is conducted in Japanese context, our approach should provide a deeper insight into a significant transnational discussion on new generations of genetically engineered crops.