The lake was situated in the Magallanes region in Patagonia and was fed by water, mostly from melting glaciers.
It had a surface area of between 4 and 5 hectares (10-12 acres) — about the size of 10 soccer pitches.
"In March we patrolled the area and everything was normal … we went again in May and to our surprise we found the lake had completely disappeared," said Juan Jose Romero, regional director of Chile’s National Forestry Corporation CONAF.
"The only things left were chunks of ice on the dry lake-bed and an enormous fissure," he told Reuters.
CONAF is investigating the disappearance.
One theory is that the area was hit by an earth tremor that opened a crack in the ground which acted like a drain.
Southern Chile has been shaken by thousands of minor earth tremors this year.