The AER says the companies include Canadian Natural Resources Limited (TSX:CNQ), Suncor Energy Inc. (TSX:SU) and Syncrude.
Ryan Bartlett, a spokesman for the agency, says it's not clear how many birds landed in the oily wastewater ponds.
He says staff are still investigating, including checking whether the companies were operating devices they are required to use during the fall migration to scare birds away from the ponds.
Mike Hudema of Greenpeace Canada says it's "another tragic reminder of just how dangerous and deadly tar sands tailing lakes really are."
He says the government promised to eliminate them but instead they continue to grow "and not a single company is meeting the government's directive to clean them up."
Syncrude, which operates one of the biggest oilsands sites, was fined $3 million for the deaths of more than 1,600 ducks when they landed on its tailings pond in 2008.
In October 2010, more than 550 birds had to be destroyed when an early winter storm forced the birds to land on the toxic waste ponds belonging to Syncrude and Suncor.
"It is an issue that our oilsands operators in that part of the province are aware of and need to deal with every fall and are required to have waterfowl mitigation systems in place at this time of year," Bartlett said Wednesday.
"We are assessing whether their deterrent systems were operating correctly."