Armed men on Friday seized about 15 people traveling on a boat near the southwestern Colombian port of Tumaco, the navy announced.
"After the seizure, the travelers were transferred to a different boat, which sailed toward the region of Chagui, in Narino department," Admiral Hernando Wills, commander of the Colombian Pacific fleet, told reporters.
The department is known as one of the most violent areas of Colombia.
It is the site of constant clashes between right-wing paramilitary groups and the leftist Revolutionary Armed Forces of Colombia (FARC), who fight over major cocaine export routes.
Although two men have been captured, it has not yet been established who the kidnappers are, officials said. He gave no further details on the two men.
The boat on which the passengers were seized has also been recovered, Wills added.
The navy, army and local police have launched a joint operation to try to free the captives.