French scientists have been studying a colony of 18,000 pairs of the penguins in East Antarctica since 2010 and found that just two chicks survived the most recent breeding season earlier this year.
They have blamed the disaster on unusually thick sea ice, which has forced the adult penguins to travel further to forage for food leaving their chicks to starve.
Yan Ropert-Coudert, a scientist at Dumon D’Urville research station next to the penguin colony, said the region had been affected by the breakup of the Mertz glacier.
He said: “The conditions are set for this to happen more frequently due to the breaking of the Mertz glacier in 2010 that changed the configuration of the stretch of sea in front of the colony.
“But there are other factors needed to have a zero year: a mix of temperature, wind direction and strength, no opening of polynya in front of the colony.”
The polynya is an area of unfrozen sea within an ice pack.
Mr Ropert-Coudert said the next breeding season was likely to be better for the birds in terms of sea ice.
Adelie penguins live on a diet of mostly krill, a small shrimp-like crustacean.
They have been declining in the Antarctic region as climate change has reduced their ice habitat and warmings seas have affected their food.
Four years ago the same colony, which then numbered 20,196 pairs, failed to produce a single chick.
Last year the Convention on the Conservation of Antarctic Marine Living Resources (CCAMLR) agreed to create the world’s largest marine sanctuary covering more than 600,000 square miles in the Ross Sea area of Antarctica.
But time ran out on a second proposed protected area in East Antarctica, covering the area where the penguins died.