The flooding might have caused due to a perforation made in a subterranean water source during the mine activities, reported Reuters.
Amaga environmental director Carlos Mario Usma was quoted by the news agency as saying: "We know that all the miners are dead.
"They were trapped at more than 200m, and the cavern is completely flooded."
Amaga mayor office official Isabel Posada said: "The mine flooded, 12 people were trapped, 28 managed to escape.
"We are waiting for the recovery of the bodies."
Gold and coal mines accidents have been increasing in Colombia due to growing illegal mining and failure to comply with safety standards, reports say.
The country reportedly has 14,000 mines, of which over 50% operate without proper permits, according to Mining.com.
The incident comes after the country’s worst coal mine blast in June this year.