In a statement released on Tuesday night, Baqaei offered his sympathies to the families of the victims, as well as the people and government of Colombia, and wished those injured and affected by the incident a speedy recovery.
Emergency responders are racing to find survivors after a magnitude 7.4 earthquake struck western Colombia, killing more than 200 people.
The Colombian government has declared a national disaster and world leaders have offered assistance.
The death toll is likely to rise, with more feared trapped under collapsed buildings.
The magnitude 7.4 quake struck at 07:34 (12:34 GMT) on Tuesday at a depth of 103km in Chocó province. It was felt across an enormous area, stretching for hundreds of miles across western Colombia.
Many of the deaths have been concentrated in Cali, Colombia's third most populous city.
At least 900 people have been injured in the quakes.