The suspected rebel attack in the northern La Guajira region was the fifth on the railway this year, with previous attacks causing days of railways closures and export delays.
Local media, citing military sources, have laid the blame for the attack on terrorist group the Revolutionary Armed Forces of Colombia, known as FARC.
At the time of publication, Cerrejon had not placed blame on any specific group for the bombing and no group had claimed responsibility.
FARC has been in peace talks with the government for six months aimed at ending 50 years of armed conflict. But there has been no cease fire deal amid negotiations.
The governor of La Guajira Juan Francisco Gomez tweeted: “We must reject violent acts in La Guajira. The violent ones will not trap us.”
Cerrejon is jointly owned by Glencore Xstrata, Anglo American and BHP.
Colombian coal production and exports have taken a battering this year, with a month-long labor strike at the Cerrejon complex and a temporary suspension of Alabama-based Drummond’s port load-out operations after the producer allegedly dumped coal into the water after a vessel accident.