The company, a joint venture between Anglo American, BHP Billiton and Glencore Xstrata, reported 33 million tonnes for the year, down from 34.6Mt the previous year.
“On top of a consistent fall in coal prices in the last three years came the 32-day strike and an increasing number of terrorist attacks on the railway line,” Cerrejon said.
Exports totalled a higher 33.5Mt in 2013, up 2% year on year.
On a more positive note, the company said it was projecting a rise in output and exports in 2014, a plan largely hinging on coal prices.
The Cerrejon complex is made up of a mine in the northern province of La Guajira along with an owned railway and port.
The company says it intends to obtain expansion licences “as far as market conditions permit” as it looks ahead to a new year.
It already has the mandatory enclosed conveyor belt loading system to fill ships at its port, meaning no disruptions like neighbour Drummond.
The infrastructure has been in place since the project commenced production.
Colombia is the fourth-largest worldwide coal exporter.
Cerrejon alone paid 1.16 trillion pesos ($A672 million) to the Colombian government in royalties during 2013.