Friday's raids were in retaliation against efforts to suppress protests by coca farmers' over a government campaign to eradicate their plots, according to officials.
"Those behind these attacks are wrong if they think they can distract the government's attention from [eradication] operations in the south of the country," President Ernesto Samper said.
Under the military alert, security forces were ordered to remain in their barracks and patrols were stepped up.
At least 94 guerrillas, police, soldiers and civilians were killed in the attacks. Officials said the death toll could rise. In one assault - the single bloodiest clash in years - hundreds of guerrillas overran a military base near the border with Ecuador. At least 34 soldiers were killed and 20 wounded, said General Harold Bedoya, the army commander.
A military source said more than 50 soldiers were killed in the attack at the remote jungle base in Las Delicias, 340 miles south of Bogota. The bodies were not discovered until Saturday. Rebel casualties in that battle were not known.
At least 33 police and soldiers and 25 rebels were killed in other clashes, said Defence Minister Juan Carlos Esguerra. Rebels, who control many rural areas but pose no threat to the government, escaped before army reinforcements arrived.
Authorities blamed guerrillas of the Revolutionary Armed Forces of Colombia. The group, the oldest and largest of Colombia's rebel groups, has thousands of fighters.
In past weeks, tens of thousands of peasants have gathered in southern Colombia to protest against government plans to destroy coca, the plant used in cocaine processing. At least 12 civilians have been killed in the violence. Authorities accuse the guerrillas, who say they represent Colombia's poor, of provoking often violent protests to protect drug-trafficking. Protesters say that growing coca is the only way they can make a living.
"They [the rebels] are defending their interests in their coca cultivations," said Holdan Delgado, chief of the armed forces. "This is truly revenge for the number of laboratories destroyed and crops affected."
Delgado said the jungle battalion attacked in Las Delicias had recently been successful in destroying cocaine labs.