For successful breeding, pairs need a stable ice shelf to last from April, when they arrive and lay a single egg, until December, when chicks fledge and the penguins move to the open sea.
In 2016, the ice sheet broke up in October, months before the chicks were ready to leave. There was no breeding there in 2017, and only a little in 2018.
Some of the pairs appear to have relocated; the nearby Dawson Lambton breeding site, which previously hosted just a few thousand penguins, saw 11,117 pairs in 2017 and 14,612 in 2018, the study said.
Dr Phil Trathan, co-author of the study, said it was impossible at this stage to specifically attribute the changes in Halley Bay to climate change, but said the size of the breeding failure there was "unprecedented".
Ice conditions in Halley Bay were stable for at least 60 years and it was previously thought to be shielded from the effects of climate change.