According to the company, the attack was carried out at around 1:39 pm local time (18:39 GMT) on Saturday, in the municipality of Orito, in Colombia’s Department of Putumayo.
"The attack caused a rupture of the pipeline and oil spill in the sector, which affected the Guamues River," Ecopetrol said in a statement, released on Twitter.
The company has notified the local Risk and Disaster Management authorities and is taking emergency measures to prevent further contamination of the environment.
Ecopetrol did not say who was behind the attack.
According to the company, the Transandino pipeline has come under 19 attacks this year.
In 2016, another oil pipeline owned by Ecopetrol came under attack, also resulting in river contamination. The bombing of the pipeline in Colombia’s Arauca Department led to an oil spill into the Bojaba river near the border with Venezuela.