International Criminal Court (ICC) prosecutor Luis Moreno-Ocampo has refused to meet Ugandan rebel Lord's Resistance Army (LRA) representatives.
Mr Kony remains in DR Congo because of the ICC warrant
The LRA lawyers want to try to get war crimes indictments lifted against three rebel leaders before signing a peace deal to end its 22-year rebellion.
"The arrest warrants issued by the court... remain in effect and have to be executed," Mr Moreno-Ocampo said.
The government wants the rebels to demobilise before approaching the ICC.
The rebellion has left thousands of people dead and nearly two million displaced.
The rebels are notorious for abducting children to be used as fighters, porters and sex slaves.
The rebels and government have been holding talks in Juba in southern Sudan and have signed a series of documents in the last few weeks in the lead up to an expected comprehensive peace agreement.
One of the accords deals with justice and accountability, and it was agreed a special division of the Uganda High Court will be set up to try those accused of serious crimes.
But the rebels want further assurances and indicted LRA leader Joseph Kony, who remains in hiding in the remote north-east of Democratic Republic of Congo, says he will not sign the agreement unless the warrants are lifted.
"Should the LRA indictees through their legal representatives wish to challenge the admissibility of the prosecutor's case... they can do so by making an application to the judges," an ICC statement said.
The government is anxious for an agreement to be reached by the end of March.
"The court is in a very difficult position," Groningen University law lecturer Andre de Hoogh told Reuters news agency.
"To be seen to drop the case because there is a peace process would seriously undermine its credibility.
"The best way to get out of it would be for the UN Security Council to ask it to suspend the investigation."
Mr Moreno-Ocampo also expressed concern at recent attacks committed by the LRA rebels, who have left assembly camps in southern Sudan and trekked towards the Central African Republic.