In spite of growing interest in neuroethics, the process of research and development (R&D) is not focused enough on the context of ethical, legal, and social issues. These processes present a unique and largely overlooked opportunity to integrate ethical and societal considerations into interactions with these technologies. We implemented a research ethics consultation during the R&D phase of Japan's national project for brain-machine interfaces; our goal was to capture the ethical and social concerns of researchers in the early stages of R&D. Furthermore, we analyzed the project's structure and found two specific features related to the researchers' ethical and social concerns: (1) the segmented structure of the project and (2) the nested structure of the project. We argue that this insight has the potential to provide neuroethics with a better understanding of R&D as well as more effective intervention strategies.