Colombian Interior Minister Carlos Holguin confirmed that six people were killed by falling rocks and earth on a highway between Bogota and Villavicencio.
The quake started around 2:20 p.m. (19:20 GMT) and was centered about 30 miles (50 kilometers) southeast of the capital, the U.S. Geological Survey said.
It struck at a depth of just 6 miles (10 kilometers) and lasted for about 40 seconds. Shallower earthquakes are felt more strongly than those that occur deep in the earth.
A number of smaller aftershocks were felt over the next hour.
Many people fled buildings fearing they could collapse and anxiously waited on the streets of Bogota. Phone systems were down briefly and calls to officials went unanswered.
President Alvaro Uribe ordered officials to assess the damage quickly "to learn how to help the community."
Emergency crews reported that a church in Puenquetame, about 20 miles (35 kilometers) southeast of Bogota, suffered serious structural damage, according to Luza Amanda Pulido, director of the president's disaster office. Some homes were also damaged.