Mystery surrounds the precise fate of thousands of Adelie penguins which apparently disappeared from Cape Denison, Antarctica, after a 2900-square-kilometre iceberg grounded near their home in Commonwealth Bay.

While scientists from the Australian Antarctic Division (AAD) assess the state of the colony, one expert says there are three possible explanations.

Dr Michelle LaRue, a research ecologist at the University of Minnesota, was part of the team that conducted the first global census of Adelie penguins, using remote sensing methods and analysis of high-resolution satellite imagery. She said the Cape Denison penguins could have skipped breeding, died or moved, either permanently or temporarily.

"While I don't know what happened ... my best guess is that their fate was a combination of the three," she said.

A count during the Australasian Antarctic Expedition of 2013-14 found 5520 pairs at Cape Denison, down from an estimated 94,254 pairs at Cape Denison and the nearby MacKellar Islets censused by Dr LaRue's team in 2011, several months before the iceberg grounded.

Research published in the journal Antarctic Science linked the decline to the expansion of fast ice – sea ice attached to the shore – which formed after the iceberg's arrival, forcing the penguins to walk 60 kilometres to forage in open water. It concluded that the colony could be gone within 20 years unless the sea ice broke out or the iceberg, known as B09B, shifted.

It showed the "devastating impact of a mega-iceberg stranding event," said Chris Turney, professor of climate change and earth sciences at the University of NSW, who led the expedition.

"Of the adult birds reaching the colony, few were successfully breeding in 2013, with the death of many young all too evident," he said. "As for the missing adult birds, we don't know how many are missing or where they are. We suspect they have stayed at sea and missed breeding in the meantime."

Dr LaRue said Adelie penguins usually return to the same place to breed, but after a huge iceberg grounded at Ross Island in 2001, the local penguins moved around much more.

"I suspect many of [the Cape Denison penguins] moved to a nearby colony, especially since in the journal article the authors mention that a nearby colony is actually thriving," she said.

​"The question for me right now is, 'Where did they go?' Knowing that 150,000 fewer animals are at a location is really interesting from a research perspective because it could provide further insight into population dynamics of the species."

The inaccessibility of their colonies makes counting Adelie penguins a challenging task, and AAD scientists emphasised the importance of "using rigorous and standardised methods" to assess population change.They found that Adelie penguin counts at the MacKellar Islets in 1913 and 1931, considered a benchmark of previous populations in the Antarctic Science paper, "lacked rigour and should not be used to assess long-term change".

"Counts of populations collected rapidly or from long distances may be too low or imprecise, and this could exaggerate the conclusions of population changes," they said.

Other AAD research, also published in the journal PLOS ONE last year, found that the five main regional Adelie penguin populations in East Antarctica had increased by 69 per cent since 1980.

AAD scientists are now analysing data from a remote time-lapse camera which monitored the Adelies at Cape Denison from January 2013 to January this year, providing information on breeding success, nest failure rates and colony attendance.

Its scientists also directed a thorough penguin population survey by the Mawson's Hut Foundation expedition this summer. By mid-2016 they hoped to have "a more complete picture of the current state of the breeding colony and the impact that the iceberg may have had".

In good news for the penguins, imagery from a satellite sensor shows Commonwealth Bay almost free of fast ice last week. Alex Fraser and Jan Lieser, of the Antarctic Climate and Ecosystems Cooperative Research Centre, said the fast ice in Commonwealth Bay had broken out this summer, apparently after a change in the iceberg's orientation.