Environment Minister Luz Helena Sarmiento told media that the agency has assessed 7 million pesos ($US3.6 million) for the illegal dumping from the barge in Cienaga, which crews said earlier that it did to keep the vessel from sinking.
Other penalties are expected to include community or social work on the part of US-based Drummond.
The fine is the highest ever imposed on a Colombian company.
Drummond said in February in the release of its internal investigation into the incident that it was a true “industrial accident”
“[There was] no intent to harm the environment but conversely actions were taken to minimise damage to the environment,” a company statement said.
“Despite the most careful attention to detail and planning to avoid this type of incident, industrial accidents do occur.”
The producer did not identify the cause of the accident.
The Colombian National Environmental Licensing Authority halted operations at the port after the accident, but it has since reopened.
Drummond and Cerrejon are the top coal players in the Andean nation.