The attacks began on Wednesday as each side ramped up charges that the other is violating a landmark truce and have forced hundreds of villagers to leave their homes in south Sudan where the talks are underway, they said.
"We can confirm that 40 people have been killed in cold blood between yesterday and today during several ambushes," a southern Sudanese government official said.
"People have started fleeing from their homes near River Nile," the official told AFP on condition of anonymity in Juba, the capital of the autonomous region where the peace talks are being held.
In addition to the deaths and an unknown number of injuries, several vehicles have been torched and property looted in the attacks that Kampala says are the work of the LRA and the rebels blame on the Ugandan military, he said.
The surge in attacks comes as Ugandan President Yoweri Museveni prepares to visit Juba at the weekend to give a boost to the halting peace talks aimed at ending northern Uganda's brutal, two-decade war.
Southern Sudanese officials have declined to identify those responsible for the violence, but have said they occurred in areas where rebel fighters are not known to be.
"It's very confusing because the LRA is not in those areas," said Major General Wilson Deng, who chairs a team charged with monitoring the August truce between Kampala and the LRA.
The LRA put the death toll at 41 and Godfrey Ayoo, a spokesman for the rebel delegation in Juba, denied any responsibility for the attacks.
"The LRA, after consulting with its military high command, has confirmed beyond any doubt that its soldiers were not involved in the attacks," he told AFP.
"We have not declared war on anyone on Sudanese soil," Ayoo said. "We are calling for a thorough investigation into who did this and wish that the results be made public."
The Ugandan army, which has had troops deployed in southern Sudan since last year under an arrangement with Khartoum, also denied responsibility for the attacks and said the LRA was to blame.
"The LRA carried out three spontaneous ambushes," said army spokesman Lieutenant Chris Magezi. "The LRA has completely used the talks to reorganise and resume terrorising people.
"Many people were injured and some are still missing," he told AFP by phone from Gulu, the northern Ugandan town at the epicentre of the 19-year LRA insurgency. "This a severe violation (of the truce)."
Since the cessation of hostilities accord took effect on August 29, boosting hopes for the success of the Juba talks, the negotiations have been hampered by numerous delays and accusations of truce violations.
Museveni, who is due to visit Juba on Saturday, has in the past expressed interest in attending the negotiations that began in July and are believed by many to represent the best chance ever to end the conflict.
But his weekend visit will come at a critical time in the talks, which have been largely stalled since producing a historic truce in August, with both sides accusing the other of repeated violations.
On Wednesday, Kampala said the rebels were guilty of a "blatant" breach of the truce by ambushing three soldiers in southern Sudan as they were walking to rejoin their unit near Juba, killing one.
On Tuesday, the LRA said its forces would not return to two neutral camps in southern Sudan that they are to occupy for the duration of the talks unless Ugandan troops in the region were also similarly quarantined.
Tens of thousands of people have been killed and nearly two million displaced since the LRA and its elusive supremo Joseph Cony took leadership of a regional rebellion among northern Uganda's ethnic Atoll minority in 1988.
The conflict is regularly described by the United Nations and relief agencies as one of the world's worst and most-forgotten humanitarian crises.

Copyright AFP (Agence France-Presse), 2006