A geological fault is being blamed for the sinkholes in the 25 hectare lake which left fish stranded in the mud.
Local residents tried to help crocodiles, lizards and turtles which were spotted trying to escape the lake.
But they were forced to leave the protected area by police over fears that it is geologically unstable.
The bizarre incident has also reportedly caused trees to topple over and other animals to leave the area after losing their water supply.
Leopoldo Santos, the president of the commission of Laguna Om, said several species had successfully been moved to a small area where water remained.
And he added that roads to the lake had been closed off to keep people away from the area.
Some of the sinkholes which have opened up in the lake are as much as 100 metres (328 feet) across, according to local police.
The lake lies close to the famous archaeological site of Chakanbakan and in the middle of a natural reserve, known as the Jaguar Sanctuary.
Officials had been working on a project to build a wooden promenade at the lake and an access road but that scheme could now be shelved.
Meanwhile, wildlife officials have launched an investigation to determine the effects of the loss of the lake’s water on local animals and plants.