A European aid worker said more than 100 people are reported to have been killed in the attack the day after Christmas and that the Congolese military put the number dead at 120 to 150.
The accused Ugandan rebel group, which has waged one of Africa's longest and most brutal wars, denied responsibility. Spokesman David Matsanga said the Lord's Resistance Army had no fighters in the area and he accused Uganda's army of the killings.
But witness Abel Longi said he recognized the rebels by their dreadlocked hair, their Acholi language and the number of young boys among them.
"I hid in bush near the church and heard people wailing as they were being cut with machetes," Longi told The Associated Press in a telephone call from the village of Doruma, site of the church, where he owns a shop.
Ugandan military spokesman Capt. Chris Magezi said survivors and witnesses described a massacre at the church near Congo's border with Sudan, where the three nations' armies this month began an offensive to root out the Ugandan rebels, who have been fighting for about 20 years. Aid and rights groups have accused the rebels of cutting off the lips of civilians and forcing thousands of children to serve as soldiers or sex slaves.
"The scene at the church was unbelievable. It was horrendous. On the floor were dead bodies of mostly women and children cut in pieces," Magezi said.
Witnesses said rebels used machetes, clubs and swords, he said.
Magezi said 45 civilians were killed. The European aid worker, who spoke on condition of anonymity because his organization fears reprisals, said a woman who escaped from the church told them there were about 30 killed but that Congolese military forces said as many as 150 people were killed.
U.N.-run Radio Okapi quoted the governor of Congo's Oriental Province, Medard Autsai Senga, as saying the death toll had surpassed 75 and bodies still were being discovered around the church.
He appealed for aid for survivors. The aid worker said hundreds of people had fled south, deeper into Congo, while the majority of people from Doruma, a village of several thousand people, were taking refuge at Naparka, about 37 miles to the south.
The rebels appear to be retaliating against civilians for military attacks including a Dec. 14 air bombing on their main camp in Garamba National Park.
Rebel spokesman Matsanga, who spoke by telephone from Nairobi, Kenya, blamed Uganda's 105th Battalion. "They were airlifted to Congo to kill civilians and then say we are responsible," he charged. "They want to justify their stay in DRC (Congo) and loot minerals from there like they did before."
Congo suffered back-to-back civil wars from 1996 to 2002 that drew in neighboring countries in what became a rush to plunder Congo's massive mineral wealth.
Long-running peace talks between the Lord's Resistance Army and the Ugandan government have stalled. Rebel leaders seek guarantees they will not be arrested under international warrants. The rebels' elusive leader, Joseph Kony, and other top members are wanted by the International Criminal Court in The Hague for war crimes and crimes against humanity.