Mr Kony wants further assurances about war crimes indictments
Ugandan government negotiators have left the jungle venue in southern Sudan where a peace deal was due to be signed with the Lord's Resistance Army rebels.
Internal Affairs Minister Ruhakana Rugunda said they would return if the rebel group was ready to sign.
Earlier, LRA negotiator David Matsanga resigned after LRA leader Joseph Kony failed to sign the deal on Thursday.
Mediators had been gathered on the border of Sudan and the Democratic Republic of Congo for the ceremony.
The BBC's Sarah Grainger in southern Sudan says mediators and the United Nations had transformed the bush close to the venue of the signing ceremony into an elaborate camp, complete with electricity and a hot buffet and had flown in dozens of journalists to report on the event.
But officials say Mr Kony refused to come out of hiding to sign until key issues on war crimes were clarified.
The two-decade conflict has cost tens of thousands of lives and is notorious for atrocities against children.
Our correspondent says the entire peace process now looks to be on shaky ground.
"We are going back to Uganda until we are informed by the chief mediator when the Lord's Resistance Army will be ready to sign," Mr Rugunda said, Reuters news agency reports.
The LRA are notorious for mutilating victims
A "cessation of hostilities" agreement signed between the government and rebels is due to expire next week.
The Ugandan government has said circumstances will have to change drastically if it is to be renewed.
Our correspondent says there has been very little communication between Mr Kony and others at the peace talks.
Mr Kony sacked his previous negotiator in December and brought in Mr Matsanga in January.
But Mr Matsanga told journalists he was tired of the situation and did not feel he could do anything more.
He also admitted that he had not spoken to Mr Kony for four days.
Mr Kony and two of his commanders are wanted by the International Criminal Court (ICC) at The Hague for alleged war crimes.
During peace talks, which began in 2006, it was agreed that a special division of the Uganda High Court would be set up to try those accused of serious crimes.
But news agencies reported that Mr Kony wanted further reassurances about the mechanisms that would be used to try LRA members for war crimes.
The signing ceremony was first postponed last week at Mr Kony's request.
It was rescheduled to take place on Thursday at a camp in the jungle town of Ri-Kwangba in southern Sudan.