The talks stalled on Friday, barely one day after the two sides resumed the peace process, over claims by the LRA that their fighters were being attacked by the Ugandan army.
In a protest letter to the chief mediator, Riek Machar, who was also the vice president of southern Sudan, LRA delegation leader Martin Ojul accused the Uganda People's Defense Force (UPDF) of attacking their positions in Magwi in eastern Equatoria, southern Sudan.
The LRA delegation boycotted the talks for a second day on Saturday.
The Ugandan government has refuted the claims. "We denied responsibility for the attacks," Okello Oryem, the state minister for international affairs and a member of the government team in Juba, was quoted by Sunday Vision as saying.
Chissano, the former president of Mozambique, on Friday morning traveled to Kampala to consult with Ugandan President Yoweri Museveni. He flew back to Juba the same day and held a closed meeting with the chief government negotiator and Interior Minister, Ruhakana Rugunda.
He met with the LRA delegation on Saturday morning, in an attempt to have the two parties meet. But no breakthrough has been made yet.
The government, on the other hand, protested to the mediator that a group of LRA fighters were moving back in a "provocative manner," contrary to the provisions of the latest cessation of Hostilities Agreement.
According to the Aug. 26 truce, the LRA fighters were supposed to assemble in two places in southern Sudan: Owiny Ki-Bul for rebels east of the Nile, and Ri-Kwangba for fighters west of the Nile. At the rebels' request, an addendum was made, allowing them to gather only in Ri-Kwangba.
"We have information that 50 LRA fighters are moving from the west (Ri-Kwangba) to the east. This is a blatant violation of the current agreement," said the spokesman for the government team, Bahoku-Barigye.
"If there is any movement of LRA troops to take place, it should be from the east to the west. They want to provoke a situation in which we attack them," he added.
The talks mediated by the southern Sudan authority have been seen the best chance to end a 20 year conflict in northern Uganda, where the LRA's insurgency has left tens of thousands of people dead and over 1.4 million internally displaced.
The peace process has, however, been marred with mutual accusations of the two parties. The rebels withdrew from the Juba talks early this year, demanding for the change of the mediator and venue.
Only after intensive multilateral coordination involving UN agencies and the involvement of observers from several other countries on the continent in the talks, the rebels agreed to come back to the negotiation table in Juba last week.