Challenges/Problems Faced By the Council

Political instabilities in some parts of Uganda like the Kony war in Northern Uganda which went on over 20years so much affected the activities of the council.
Some places are too remote with poor transport which has also limited the movement of the council officials to different places.
There is lack genuine trust among the three interfaith churches i.e. they are united just for formality.
It also faces political threats in some of there activities i.e. some times it is forced to stay away from politics.
The long history of fighting violence between the karamojong and itesotes has made hard for the council to reconcile the two groups.
Unemployment and poverty among the people has made it hard for the council to fight immoral practices like corruption and prostitution.
cultural rigidities and conservatism among the karamojongs who look at cattle rustling as part of their culture and way of life has led to continued inter-tribal fighting
It has faced a problem of commitment on the side of the rebels during the process of peace talks in the Northern Uganda war.
Removing of small arms from the karamanjongs was sometimes done secretly by the government security organs which interfered with the council work.