At least 40 people are thought to have died, including several civilians, in clashes between government troops and guerrillas in the town of Valencia, Cordoba province, 950 km (590 miles) north of the capital Bogota.
The rebels, from the Revolutionary Armed Forces of Colombia (FARC), were also blamed for a mortar attack on an airport in the town of Saravena, 350 km (215 miles) northeast of Bogota, which caused heavy damage and injured several soldiers and civilians.
Mr Uribe has pledged to crack down on the rebels with the full backing of the US, which has given Colombia more than $1bn of military aid and promised more.
During Mr Uribe's electoral campaign, FARC declared him a military target.
The BBC's Jeremy McDermott in Bogota reports that the Colombian secret police, the DAS, on Monday arrested six FARC members in the capital who were carrying guns with telescopic sights and ammunition.
In the city of Medellin, two mortar rounds launched at a police station fell into a residential neighbourhood but failed to explode, before being defused by explosives experts, the Associated Press news agency reported.
Rebels also downed electrical towers in the city, leaving residents temporarily without power and a car bomb exploded, causing damage to buildings.
In the resort town of Cartagena, a bomb stashed in the bathroom of a government building exploded, slightly injuring three people.
Security tight
Security in Bogota has been tightened ahead of Mr Uribe's inauguration, with 20,000 extra security personnel deployed in the city.
Several security rings have been established around the presidential palace where the handover of power will take place.
All flights over Bogota have also been banned for the duration of the ceremony and security has also been stepped up in other main cities.