Millions of people have been displaced by fighting
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Human rights activists say a new deal between Ugandan rebels and the government may result in "sham" trials.
Amnesty International called for suspected war criminals in Uganda to be handed over to the International Criminal Court (ICC).
The call comes after a new deal was announced between Lord's Resistance Army rebels and the government.
They agreed to set up a special court to deal with alleged war crimes - one of the obstacles to a final peace deal.
But Amnesty said the deal was contrary to international law because arrest warrants had already been issued for the suspects.
"Many of these people have been charged with horrific crimes - and international warrants have been out for their arrest for more than two and a half years," said senior legal adviser Christopher Keith Hall.
"They must be handed over so that their guilt or innocence can be determined once and for all. The people of Uganda deserve no less."
The government said the deal meant a final peace agreement could now be signed "soon".
The LRA have refused to disarm, while three of their leaders are wanted by the ICC.
The government has given the LRA until 28 February to end the war which has uprooted some two million people.
Around 20 years of fighting with the LRA has killed tens of thousands of people and uprooted some two million people.
The LRA are notorious for mutilating victims and kidnapping children to be fighters, porters and sex slaves.
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