The Colombian Navy said in a news release on Wednesday that a fishing boat saved seven men and two women but the boat that sank was carrying 120 people leaving Ecuador illegally when it had capacity for only 15.
"The Colombian Navy immediately began a search and rescue operation to find the bodies of the shipwreck victims using an airplane and marine patrol launch," it said.
There was no immediate word on where the passengers were heading. Illegal immigrants have in the past been jammed into boats leaving South America to reach Central America and then continue to the United States by land.
The Colombian statement said the navy received word of the sinking on Tuesday evening but did not indicate when the sinking occurred or whether the missing were feared dead.
The disaster happened more than 160km off the coast of Colombia.
In August 2004, a US Coast Guard ship patrolling international waters intercepted a disabled Ecuadorean boat carrying 106 migrants.
Immigrant smuggling has become an industry in Ecuador, where 60% of the nation's 12 million citizens live in poverty and many dream of a better life in the United States.