By Tim Cocks

KAMPALA, July 4 (Reuters) - Uganda said on Wednesday it will set up a special tribunal to deal with war crimes allegedly committed by northern rebels during a 20-year conflict, but that it would not handle charges of abuse by the Ugandan army.

The Lord's Resistance Army (LRA) guerrillas immediately rejected the move as a breach of a deal signed on Saturday that aims to end a war that has killed tens of thousands of people and uprooted nearly 2 million more.

Internal Affairs Minister Ruhakana Rugunda, who has led Ugandan government negotiators at nearly a year of peace talks in neighbouring southern Sudan, told journalists both parties would have to agree on the details of penalties for crimes.

"It would be premature for us to give specifics. Sentences, courts, etc, will only be arrived at after consultations by ourselves and the LRA," he said.

At the weekend, the LRA and the government signed phase three of a five-stage peace deal.

Phase three deals with accountability for war crimes and promises to use a national process, implicitly rejecting calls to hand over the rebels' top commanders to the International Criminal Court (ICC) in The Hague.

LRA leader Joseph Kony and three others are wanted for crimes including murder and using child soldiers, but say they will never make peace unless the ICC drops the charges.

"What we are working for is that all these people should be handled in Uganda," Rugunda said.

DECEIT?

But he said only LRA fighters will face tribunals, because the national army, the Uganda People's Defence Forces (UPDF), already has existing courts marshal for punishing soldiers.

Rugunda said the military courts had dealt harshly with many wayward troops in the past, but LRA representatives rejected the creation of special tribunals for the rebels.

"This is deceit," the head of the LRA delegation at the peace talks, Martin Ojul, told Reuters. "Accountability has to apply to both parties, as in our agreement. Is that justice if only one side is held accountable?"

Phase three does not say whether government troops will face justice but a clause in an earlier draft saying "accountability shall apply to both state and non-state actors," was removed.

Analysts said the LRA were maybe too soft in negotiations.

"There is incriminating evidence on both parties. The terms of the agreement suggest the LRA delegation was wrong-footed," said Tim Allen of the London School of Economics, an expert on Uganda's conflict.

Leaders from Kony's Acholi tribe want the LRA to undergo a "Mato Oput" reconciliation ritual, where victims forgive a murderer after he admits his crime and pays compensation. Rights groups reject that.

"Penalties need to fit the gravity of the crimes," said Richard Dicker of Human Rights Watch. "We're not talking about pickpocketing, we're talking about mass murder, rape, mutilation."

Rugunda said the tribunal would blend "existing formal justice, which is punitive, and the traditional cultural mechanisms which promote reconciliation," but added that amnesties would be possible.

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