Many have fled after more than 100 were killed
Civilians have been streaming from the violence-hit towns north of the western provincial town of Quibdo in Choco state.
A local priest has expressed fears that thousands of people still in the area will be caught in the crossfire as the government forces try to regain control of the lawless region.
Leftist rebels from the Revolutionary Armed Forces of Colombia (FARC) have been battling paramilitaries of the United Self-Defence Forces of Colombia (AUC) for control of the area, long abandoned by the state.
In an attack blamed on FARC guerrillas, a home-made mortar bomb was dropped onto a crowded church in the Choco town of Bojaya on Thursday, killing at least 60 people who were sheltering inside.
'Terrorist' attack
The UN High Commissioner's Human Rights Office in Colombia has issued a statement defining this as a war crime, while Colombian President Andres Pastrana has accused the rebels of genocide.
Pope John Paul II condemned the attack as an "act of terrorism" by rebels who "respect neither people nor sacred places".
Other victims were killed in crossfire between the rebels and the AUC, in an area without police or army posts.
Mr Pastrana held emergency security talks in Quibdo and has deployed thousands of troops in the region, amid widespread anger at his government's failure to act sooner.
Church bomb
Survivors of the fighting at the river towns of Bojaya and Vigia del Fuerte who reached Quibdo recounted scenes of horror.
"When the bomb exploded, everybody that could went running, they ran out," said one survivor of the church attack from his hospital bed.
"Those who couldn't, well, they were buried... My girlfriend didn't make it out," he said.
The Colombian army, which is believed to be sending about 4,000 soldiers to the area, estimates there are between 800 and 1,200 FARC guerrillas and 500-600 AUC fighters there.
'Warning ignored'
As the heavily armed soldiers set off from Quibdo, local people voiced anger at the army's three-day delay in responding.
"The massacre has already happened and now Pastrana gets here," shouted Saul Olaya, a local resident.
"Children have arrived here severely burned. It makes you want to weep," he said.
"If there is a military solution, why didn't they use it two years ago when they know about the presence of armed groups?" asked the priest, Albeiro Parra, in an interview with a local newspaper.
Colombia's human rights ombudsman, Eduardo Cifuentes, blamed the tragedy on the lack of government forces in the region.
United Nations officials have said they warned the government that a tragedy was about to occur after reports that AUC forces had entered the area.
"It is lamentable that the government authorities ignored the early warning," the UN said in a statement quoted by The Associated Press.
'Emergency'
Bojaya's mayor, Ariel Palacio, has said the town is facing a sanitary emergency, with large numbers of the injured still waiting for treatment, and decomposing corpses piling up.
Helicopters have been transporting casualties to the city of Medellin.
At least 35,000 people have been killed over the last decade of violence in Colombia, and about two million people have fled their homes.