Lieutenant Chris Magezi, a spokesman for the Ugandan army, said on Saturday the death toll from the massacre in Lira district could exceed 100.
"Scores of civilians were killed at around midnight on 6 November in Alanyi and Awayopiny villages in Lira district," Magezi said.
"Probably more than 100, but this is pending details of the exact death toll," Magezi said, responding to queries what the final toll could be.
Missionaries in the region said villagers were forced to watch as rebels beheaded the corpses of civilians they had just killed.
The guerrillas, led by Joseph Kony, are feared for their brutality and for abducting thousands of children to use as sex slaves and frontline fighters in the east African country's long-running civil war.
"Scores of civilians were killed at around midnight on 6 November in Alanyi and Awayopiny villages in Lira district"
Magezi said the Lords Resistance Army (LRA) appeared to have ordered the attacks in revenge for the army's recent killing of a senior rebel commander.
The Ugandan authorities deployed more than 14,000 troops backed by helicopter gunships and tanks to crush the rebels last year, but the LRA is far from being crushed.
The rebels have actually stepped up their attacks in recent months and pushed further south towards the capital, Kampala.
The rebels say they are fighting to overthrow the government of President Yoweri Museveni. But little else is known about their other demands.