Yoweri Museveni, the Ugandan president, and his aides made no comment about the private unscheduled half-hour meeting at south Sudan's parliament building. But an LRA official said the discussion was one-sided, and that the Ugandan leader had "abused" them.
Godfrey Ayoo, an LRA spokesman, said: "He spent all that fuel in the presidential jet and all that taxpayers' money just to tell us we know nothing about Uganda and are foreigners.
"We were not given the opportunity to talk back, and after he abused us for five minutes, he just left."
Most of the LRA's negotiators come from Uganda's diaspora.
Ayoo said Museveni had tried to shake hands with Josephine Apira, the one female member of the LRA delegation, but she refused and asked him to apologise for killings by his army.
Ayoo said: "He said, 'This is rubbish' and walked out.
"It was an exchange that suggests we still have a long way to go. It was not meaningful. It did not improve things in any way."
In a speech later to south Sudan's parliament, Museveni hinted at his frustration in dealing with the LRA, who he has often denounced as fugitives, terrorists and bandits.
He hailed Riek Machar, the southern Sudanese vice-president, who is the chief mediator at the stop-start peace talks, as a "very, very persistent person".
"He knows how to deal with the unserious LRA. If it were me..." he told parliament, without finishing his sentence.
The LRA has killed tens of thousands of people and uprooted 1.7 million in northern Uganda alone during 20 years of fighting, as well as destabilising remote parts of southern Sudan and northeastern Democratic Republic of Congo.
During their insurgency the LRA has become notorious for killing villagers, slicing body parts off survivors and kidnapping thousands of children to serve the group as fighters, porters and sex slaves.
A truce signed in August by the government and the LRA raised hopes of an end to the fighting. Under the deal, the LRA were supposed to gather at two locations in southern Sudan while talks to win them amnesty continued.
But independent monitors said both sides then violated the agreement. They said that the LRA failed to assemble at the designated locations and that the Ugandan military encroached on the locations. The LRA said they had gathered, but then fled fearing attack.
Museveni had earlier landed in Juba amid tight security as helicopter gunships circled overhead. He was met by Salva Kiir, the south Sudanese president, and went straight into meetings.
He made no comment to journalists gathered at the airport, and a planned press conference was later cancelled.
The LRA's top leaders are wanted for war crimes by the International Criminal Court in The Hague, and have said they will not sign a peace deal unless the indictments are dropped.
From the outset, the talks were marred by deep mistrust on both sides, and were undermined further this week by the killing of at least 38 civilians in ambushes south of Juba.
The LRA and Uganda's military each accused the other of carrying out the attacks.