The local Tilapia fish, being raised in 50 cages in Sebu Lake, had a value of $88,000, Rex Vagas, provincial fishery coordinator, said.
He said 46.5 tons of Tilapia were found dead last Friday and 2.5 tons on Monday, Chinese news agency Xinhua reported.
Vagas attributed the massive death of fish to an "annual occurrence" locals call "kamahong," when water temperatures experience extreme increases leading to oxygen depletion in the waters of the lake.
"We ask consumers to avoid buying and eating Tilapia fish from Lake Sebu until further notice from us," Vagas said.
The provincial agriculture office blamed the low oxygen level in Lake Sebu on overstocking and water pollution, probably from fish feeds.
Fish cage operators were told to temporarily stop feeding surviving fish for at least a week to allow the lake's oxygen level to return to normal, authorities said.