Uganda's government has rejected a key rebel demand that it try to get war crimes indictments lifted against three Lord's Resistance Army (LRA) leaders.
Mr Kony remains in DR Congo because of the ICC warrant
The issue threatens a deal to end the 22-year war as the government wants an agreement to be reached by 29 February.
Government spokesman Chris Magezi told the BBC it was premature to approach the UN and International Criminal Court until rebels had demobilised.
The rebels and government have been holding talks in Juba in South Sudan.
Over the weekend, both sides signed a permanent ceasefire to come into effect 24 hours after the signing of a comprehensive peace deal.
This replaces a series of cessation of hostilities agreements that the government and the LRA rebels have renewed throughout the peace talks and which have largely restored security across northern Uganda.
Last week, a deal over justice and accountability for war crimes 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 insist the ICC arrest warrants be lifted before a final deal is signed.
LRA leader Joseph Kony, one of those indicted, remains in hiding in the remote north-east of Democratic Republic of Congo.
"Kony gave me all the authority to negotiate on his behalf but if the ICC indictments are still in place, he said he would never, I repeat, never assemble," LRA David Nyekorach-Matsanga told Uganda's Monitor newspaper.
The LRA want the Ugandan government to write to the UN Security Council and ICC to have the warrants lifted - and to have a clause to that effect put into the final agreement.
Capt Magezi said this was not possible until a full demobilisation of the rebels had occurred, but he wanted to reassure Mr Kony and the LRA team that the government would stick to its word.
"Negotiations take time, I'm sure we will reach common ground," he told the BBC's Focus on Africa programme.
While the talks have been making progress, there have been reports that some LRA fighters have left assembly camps in Sudan and trekked to the Central African Republic.
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.