WASHINGTON — It was an unexpected journey by attorneys for the elusive Joseph Kony, a Ugandan rebel commander with messianic delusions and a ghoulish human rights record. The legal delegation went on an exploratory mission earlier this month to the International Criminal Court, which wants Mr. Kony tried on war crimes charges for his role leading the Lord’s Resistance Army.

The visit to The Hague came during the final phase of negotiations between president Museveni of Uganda and Mr. Kony’s brutal and bizarre rebel army to end one of Africa’s longest-running and most vicious wars.

In addition to killing thousands, the conflict, which began in 1986, has driven close to 2 million people from their homes to languish in hundreds of squalid refugee camps. More than 25,000 children have been abducted to serve the rebel army — motivated by a fanatical Christian doctrine — as foot soldiers and sex slaves.

But before signing the peace accord — something many Ugandans had hoped would happen later this month, following a permanent cease-fire reached last month — Mr. Kony has demanded that the international court drop the arrest warrants and indictments against him and two deputies in hiding.

The court’s chief prosecutor, Luis Moreno-Ocampo, has ruled out the request to drop the 33 counts of war crimes and crimes against humanity facing Mr. Kony and his deputies.

The standoff has highlighted a debate with potentially far-reaching implications for other countries seeking to end civil wars marked by atrocity and displacement: how can international demands for justice be balanced with local demands for peace?

Humanitarian groups such as World Vision, which has a large presence in Uganda’s refugee camps, have argued that the court should step aside to allow a peace agreement to take hold across the distressed territory where they work. The groups argue that it is more important to alleviate the suffering of Ugandans, who are dying of malnourishment and disease in the cramped camps, than prosecute the rebels on the international stage.

“The key for signing an agreement is finding an exit for Kony,” John Prendergast of the Enough project, an advocacy group seeking to end genocide, said.

Mr. Prendergast has suggested that to prod Mr. Kony into signing the agreement and ending his campaigns of violence, he should be offered asylum in a third country other than Uganda or Congo, where Mr. Kony has been hiding in a remote northwestern jungle region.

But leading international human rights groups say Uganda does not have a legal system capable of punishing Mr. Kony and his deputies, meaning that a waiver of the international court warrants could result in impunity for the rebel army’s atrocities.

Mr. Kony began his rebellion in northern Uganda to regain the power his tribe enjoyed immediately after Uganda gained independence from Britain in 1962.

He has said his movement’s ideology is inspired by the Ten Commandments. But he and his cultish army of several hundred members have employed superstition and rituals, believing they repelled danger, while using crude instruments to sever lips, ears, and limbs of people suspected of not being true followers.

Mr. Museveni has pledged to create a special unit within Uganda’s high Court to manage war crimes trials, but no such unit has been established.

Mr. Museveni’s government and Mr. Kony’s army, which resumed negotiations in 2006, had planned to sign the final peace protocol by March 28. As part of the deal, Uganda’s government pledged to appeal to the United Nations Security Council to suspend Mr. Kony’s indictment for a year, once the comprehensive accord was signed.

The Security Council has this authority, but can do so only if it determines, following an assessment by the international court’s judges, that Uganda can manage the trials on its own. The international justice program director at Human Rights Watch, Richard Dicker, said Uganda would have to amend its legal code to include laws that address crimes against humanity. Amnesty International has expressed similar views.