Uganda's government says it has no authority to block war crimes charges against rebel leaders until the two sides reach a peace agreement.
Leaders of the rebel Lord's Resistance Army have warned they will refuse a final peace deal unless the charges from the International Criminal Court are dropped.
The chief government negotiator, Ruhakana Rugunda, says Uganda can ask the court to suspend the indictments only after rebel leaders sign a peace deal and admit to their crimes.
The Hague-based court has refused to drop war crimes charges against rebel chief Joseph Kony and four of his aides.
Members of the Lord's Resistance Army are accused of killing, kidnapping and mutilating thousands of civilians during their 20-year insurgency in northern Uganda.
The issue is one of several clouding peace talks between the rebels and the government in southern Sudan.
Some information for this report was provided by Reuters.