The blast Friday occurred at a coal mine in the town of Cucunuba in Cundinamarca state, some 90 kilometers (55 miles) north of Bogota, at about 2130 GMT.
One person was injured in the explosion, authorities said.
Earlier reports listed two dead and 11 miners missing in the disaster.
A rescue crew of 35 miners and seven engineers has been working "around-the-clock" in a frantic search for the missing, the National Mining Agency (NMA) reported.
"We are going to dig by hand throughout the night to try to rescue" the missing workers, Wilson Garcia, director of the emergency response unit in Cundinamarca, told AFP late Friday.
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President Juan Manuel Santos, who was wrapping up a visit to France, used Twitter to express his "solidarity with the victims."
Officials said they do not know what caused the explosion.
The country has seen an increase in illegal mining in recent years.
A total of 28 mining emergencies were reported in Colombia in the first five months of this year, leaving 23 dead and 33 injured, according to an NMA report. Sixty percent of the accidents occurred in coal mines.
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There were 114 mining emergencies last year, causing 124 deaths, the report said.
Colombian coal production hit a record 90 million tons last year, according to the Ministry of Mines and Energy.
Colombia, a major world supplier, provided more than 70 percent of US coal imports.
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