The 29-year-old actress told The Daily Telegraph: "There were girls on the longlist and I think it's really odd that girls haven't made it where guys have.
"We'd hope that gender doesn't really come into it and it's about the body of work that they produce that year, but it seems that hasn't been the case."
The longlist for the award included Jessica Chastain, Felicity Jones and Hunger Games star Jennifer Lawrence. The official nominees for the award were Adam Deacon, Chris Hemsworth, Chris O'Dowd, Eddie Redmayne and Tom Hiddleston, with Deacon proving triumphant in the category.
This is the first instance since the Rising Star award was started six years ago that a female has not been included in the shortlist. It has been awarded to actresses Eva Green and Kristen Stewart in the past.
Hayley Atwell is best known for her performances in Brideshead Revisited and Captain America. She has expressed interest in being a part of the sequel to Captain America, but it is unclear if her character will make a return when filming begins later this year.
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Watch Hayley Atwell in the trailer for Captain America: The First Avenger below: