The government side has been angered by what it regards as belligerent remarks by rebels at the opening ceremony.
Correspondents say the Ugandan delegation at one stage threatened to return home on what was scheduled to be the first full day of talks.
The talks are considered north Uganda's best chance for peace in years.
Thousands have died in the two-decade conflict between rebel Lords Resistance Army (LRA) and the government, and some two million have been forced to flee their homes.
At the opening ceremony on Friday night, delegates from the LRA warned that the Ugandan government would be in for a shock if it thought the rebels were about to surrender.
None of the top LRA leadership are attending the talks
Our acceptance of these peace talks should not be interpreted to mean that the LRA can no longer fight or that we are now military weak. No. We are not," said LRA spokesman Obonyo Olweny.
"Should they resume in Kampala to choose the path of violence and militarism in the belief that they can settle the current conflict in the battlefield by decisively defeating the LRA then they shall be in for a rude shock."
The head of the government delegation, Ruhakana Rugunda, was more conciliatory, saying that they had come to negotiate and conclude peace.
The rebels - who have been promised an amnesty - have not sent their top leaders to the negotiations, but say they are willing to sign a ceasefire.
Few of the 17-member delegation that arrived in Juba on Thursday have combat experience and many of them are based abroad.
It is debatable whether they have the influence to negotiate on behalf of the leadership in the bush, says the BBC's Jonah Fisher in Juba.
LRA leader Joseph Kony and four of his commanders are wanted for war crimes by the International Criminal Court (ICC).
Ugandan President Yoweri Museveni has offered them a full and guaranteed amnesty as long as they renounce violence.
BBCGüncelleme Tarihi: 20 Eylül 2018, 18:16