Starting with the assessment of the humanitarian response to Japan’s “3/11” triple disaster of 2011 (earthquake, tsunami and Fukushima nuclear disaster) provided by civil society actors, this article explores the problem of the capacities and capacity building of Japanese non-governmental organisations (NGOs) working in relief and recovery sectors and beyond. The article uses a case study of the TOMODACHI NGO Leadership Programme (TNLP) (2013–2016) to critically assess ongoing capacity-building challenges facing the Japanese NGO community. The article proposes that 3/11 was a significant critical juncture that spurred further efforts to improve NGOs’ institutional capabilities and preparedness. It further contends that the TNLP contributed to delivering humanitarian principles, safety and security, and advocacy-related training opportunities for members of the Japanese NGO community. The capacity needs of Japanese NGOs and measures to address these, as illuminated by the post-3/11 initiatives and the TNLP presented in this article, also demonstrate the limited commitment of the Japanese government to support the growth of NGOs. Finally, the utility of joint projects by Japanese and Western NGOs for both delivering capacity development and advancing mutual understanding is discussed on the basis of relevant TNLP activities.