This paper explores the role of negative emissions technologies (NETs) in energy systems, bioenergy with carbon capture and storage (BECCS) and direct air capture (DAC) with geological carbon storage (DACCS) in particular, using a bottom-up energy system model TIMES-Japan that participated in the 35th study of the Stanford Energy Modeling Forum (EMF 35 JMIP) focusing on the energy transitions for the long-run climate goals. Modeling results show that large-scale deployment of NETs is essential to achieve the net-zero vision of Japan’s long-term strategy, however, these NETs might not be enough in the case of the highest energy service demands. Within the feasible solution space, earlier deployment of BECCS with domestic biomass can contribute effectively to achieve the target with the support of the DACCS at the later period if both technologies are available. It shows feasible results without DACCS only in the lowest energy service demands, implying the importance of urgent research, development, and deployment of DACCS. Furthermore, this study shows that earlier deployment of DAC system with CO2 utilization in fuel production is a cost-effective way to lead the large-scale deployment of the DAC as NETs.