Typhoon Morakot brought unprecedented rainfall that impacted Taiwan more harshly than ever before in the island’s recorded history, consequently resulting in severe loss of life, destruction of property, and danger to the cultures of indigenous peoples. In the face of such a traumatic event, the indigenous peoples need spiritual care and counseling to help recover from the fright, in addition to dealing with urgent issues such as relocation, schooling and employment. The successive reconstruction and restoration of indigenous affected regions is an important challenge for the continuance and development of indigenous cultures. This paper argues that a human rights approach towards the post-disaster reconstruction of indigenous affected regions should be built upon safeguarding the indigenous cultures, the people as a whole and their derivative social systems, the ecological balance, and the communication of beliefs. Thus, this paper takes an analytic-institutional approach to examine the implementation of the Post-Typhoon Morakot Reconstruction Special Act to protect indigenous peoples’ rights in accordance with the Indigenous Peoples Basic Law. Also, this paper will deliberate on related international instruments by putting forward concrete recommendations based on the analyses of human rights and indigenous culture-based reflections.