In 1999, the Government of Indonesia established Government Regulation (GR) 32/1999 on the Procedures for the Implementation of the Rights of Inmates which has been most recently amended by GR 99/2012. However, the establishment of GR 99/2012 creates complication and unfairly discriminates against inmates committing extraordinary crimes (terrorism, drug abuse, corruption, crimes against the security of the state, crimes against humanity and other transnational organized crimes) impeding such inmates to file for remission and parole. This paper examines the consistency between the implementation of GR 99/2012 and the concept of criminal punishment in Indonesia. It is a summary of empirical juridical research that reports on the influences of GR 99/2012 on inmates in correctional institutions. Data used for this research was obtained from interviews, observation, desk reviews and focus group discussion with government officials. Based on the findings, it can be inferred that GR 99/2012 has impeded the fulfillment of inmates’ rights to file for parole and remission due to complicated procedures, additional fines, and multi interpretation of the regulation. Furthermore, it affects the aggravation of overcrowding, violations against inmates’ rights, and illegal practices within the process. Based on the analysis discussed in this paper, GR 99/2012 is inconsistent with the concept of criminal punishment in Indonesia because it impedes inmates’ reintegration into society. This paper proposes that GR 99/2012 should be revoked and revised in accordance with the spirit of Corrections Act and to create synergy among law enforcers in fulfilling inmates’ rights.