Major challenge faced by FOHRID in implementing its programs was inadequate budget in comparison to the planned programs. After the political change of April 2006, Nepal was engaged in the political issues such as formulation of new constitution and state restructuring. Difficulty was felt in convincing the target groups to address impunity and to interlink this issue with human rights movement as was proved now a major cause of human rights violation in Nepal. Problems were also created by lack of understanding in the major stakeholders and lack of sensitivity on impunity. Lack of political will and the indifference of political parties made it difficult to determine actions to address political impunity.

Transitional phase is unduly prolonged in Nepal. Unstable political situation of the country had somehow negative impact to the past programs. State mechanisms have been weakened. Dozens of armed groups have emerged to fish in the troubled water of politics. Incidents of murder, violence, abduction, robbery and human rights violation have increased. Civil and political rights as well as the economic, social and cultural rights are being challenged. International human rights instruments including treaties, Conventions, Covenants, Optional Protocols have not been effectively implemented at the domestic level. Impunity is institutionalized and is protected from the state and political level. There is suspicion on whether peace process will succeed or not.