For his short program, Shulepov used different music and wore a dark top that could be opened to reveal a red shirt over black pants.
"The ISU regrets that by error the wrong costume (Free Skating instead of Short Program costume) of Mr. Shulepov has been presented for voting," the organization said in its statement.
When the organization announced on Twitter on Sunday that it was opening voting to the public for its inaugural ISU Skating Awards, it received dozens of replies demanding that Shulepov's "Schindler's List" costume be removed.
"His costume is offensive to people like myself who lost family," one Twitter user wrote. "Genocide is not entertainment. It's not sport."
"While we understand the need for skaters to be creative in their choice of costumes, Anton Shulepov's apparent decision to evoke painful Holocaust imagery as part of his routine was insensitive and offensive," Jonathan Greenblatt, CEO of the Anti-Defamation League, said in a statement via The Guardian.
"We are surprised that the International Skating Union initially posted a picture of this costume as a nominee for 'costume of the year.' Yellow Stars of David or other concentration camp imagery have no place in figure skating."
The ISU did not immediately respond to a request from The Post for comment on whether the outcry that followed initial announcement of award voting influenced the switch in Shulepov's nomination in the category.
The "best costume" category is among four open to voting by the public, as well as to ISU and media members.
Following the online voting, which is open until Feb. 10, three nominees in each category will be announced on March 10. The awards ceremony is set to be held March 22 at Montreal's Bell Centre, site of the 2020 World Figure Skating Championships.