Authorities did not yet 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.
"At the moment we officially have nine people who have been found dead" and "approximately 28 people reported missing," said Margarita Moncada, head of the disaster prevention department of the Antioquia regional government.
She said the boat was carrying 170 people, most of whom were rescued by other boats or escaped by themselves.
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"It sank extremely quickly. It all happened in a few minutes," said a fire service captain involved in the rescue effort, Luis Bernardo Morales.
One helicopter from the air force and two from the army went to help in rescue operations, the military said.
The reservoir is 68 kilometers (40 miles) from the city of Medellin and one of Antioquia department's main tourist draws.
One woman who survived said that the two lower decks were "too crowded" and there were "lots of children" on board.
"We started to feel like the boat was going to capsize," said the woman, who appeared on television but was not identified.
The Antioquia regional government said on Twitter that 24 people caught in the wreck were being treated in hospital.
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Video circulating on social media showed the ship going down and dozens of other vessels approaching it to try to rescue people.
"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," said Morales, the fire captain.
He said rescuers were having difficulty reaching the reservoir by road due to heavy traffic on the major Medellin-Bogota highway.
Guatape fills with tourists on long weekends like this one, since Monday is a holiday in Colombia.
Visitors come for one- or two-hour cruises on the reservoir and to fish and jet-ski.
The national fire service said it was dispatching firefighters from six 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 Blu Radio.
President Juan Manuel Santos said on Twitter the air force and rescue services were deploying to deal with the "emergency."
Agradezco a @COL_EJERCITO, @armadacolombia, @DNBomberosCol, @FuerzaAereaCol y @UNGRD por su trabajo en emergencia de Guatapé. pic.twitter.com/b7dqegOoFa
— Juan Manuel Santos (@JuanManSantos) June 26, 2017
"We are ready to provide the assistance required," he wrote.
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