The conflict, between the kidnapped child soldiers of the Lord's Resistance Army and the Ugandan Government, was described by the UN in November as the "biggest neglected humanitarian emergency in the world today".
More than 800,000 displaced people live in "protected camps", and around 22,000 children have been abducted since 1990 - 6,000 in the first half of 2003 alone.
The Church Mission Society, which launched a 'Break the Silence' campaign last year to alert the public to the war, has asked other international NGOs working in Uganda to form a united front.
The society met with Oxfam, Christian Aid, Human Rights Watch, Amnesty and Christian Solidarity Worldwide earlier this month to discuss collaborative working. Much of their efforts will focus on lobbying governments and the UN to create international pressure to end the conflict.
A Christian Aid spokeswoman said: "People are going to have sit down and talk. There could be intermediaries between tribal religious leaders and the top commanders of the Lord's Resistance Army, or an impartial mediator like George Mitchell in Northern Ireland."
The Church Mission Society is calling for UN peacekeepers to be sent to the country to create a buffer zone between the Lord's Resistance Army and President Yoweri Museveni's forces.
Its head of media Jenny Taylor said: "All of the agencies have developed different areas of expertise. The society has traditionally been a relational organisation - our links with religious leaders will be uniquely strong, though we are not set up for advocacy work. But Human Rights Watch, for example, is a global organisation with a presence at the UN."
All agencies are opposed to attempts to end the conflict militarily.
But negotiations with the LRA's reclusive and brutal leader Joseph Kony will prove difficult. Kony is committed to overthrowing the Museveni government and replacing it with a regime based on the 10 commandments.