Officials did not say what caused the four-deck Almirante to go down in the El Penol reservoir in the tourist town of Guatape, where Colombian and foreign tourists take leisure cruises.
"So far we have three people deceased" and "approximately 30 missing," police commander Jorge Hernando Nieto said on BluRadio.
The air force said a helicopter was on its way to help in rescue operations.
The reservoir is 68 kilometers from the city of Medellin and one of Antioquia department's main tourist draws.
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"The situation looks serious," said an official with the Antioquia government.
The official said rescued people were being sent to the local hospital in Guatape.
"It sank extremely quickly. It all happened in a few minutes," said a fire service captain involved in the rescue effort, Luis Bernardo Morales.
"What we have seen in the videos is that the boat was very close to the port... And we do not know whether it was a mechanical failure, an overloading or something to do with the currents that caused it to sink."
The national fire service said it was despatching firefighters from seven towns to help.
Medellin's mayor Federico Gutierrez said he was sending a team led by a firefighting crew captain and five scuba divers.
"The area is a bit difficult to reach and various rescue and emergency teams have started joining in," he said on BluRadio.
President Juan Manuel Santos said on Twitter the air force and emergency services were deploying to deal with the emergency in Guatape.
"We are ready to provide the assistance required," he wrote.