Two armed men stashed drugs on a Zeaborn Ship Management-operated boxship while it was underway off Ecuador.
The unusual incident involving the 2,546-teu Sealand Los Angeles (built 2008) was revealed by the army this week.
The incident marks a departure from the usual practice of covert operations to attach narcotics to hulls when vessels are docked.
The army said the boxship was underway from Guayaquil to Balboa in Panama when two gunmen boarded the ship and hid 88 packets of cocaine in a container.
When the ship docked in Puerto Bolivar, a coordinated search was launched with the prosecutor's office, the anti-narcotics police and the shipping agency representing the vessel, according to daily newspaper El Comercio.
Four black suitcases containing cocaine blocks were found in a box.
No injuries were reported among the crew.
The Sinoceanic-owned ship was due to remain at the dock while an investigation was carried out.
Zeaborn has been contacted for comment.
Ecuador is not a drug-producing country, but it is considered a territory for the transit of cocaine from Colombia.
Last year, up to the end of November, Ecuadorian authorities had reported the seizure of 63 tonnes of drugs.
