The flag carrying the SS death skull symbol, which also references the Chelsea Headhunters, a hooligans' group with roots in the late 1960s, is not thought to have been waved during the game.
The Observer reported the fans carrying it were believed to have remained in central Budapest away from the stadium during the stadium, and therefore out of the club’s jurisdiction.
Any fan caught attempting to smuggle such a banner into the stadium would have risked incurring a ban from Chelsea.
In a statement on Friday after reports of antisemitic chanting emerged, a Chelsea spokesperson questioned the “brain-power” of some of its fans.
The spokesperson said: “Antisemitism and any other kind of race-related or religious hatred is abhorrent to this club and the overwhelming majority of our fans. It has no place at Chelsea or in any of our communities.
"We have stated this loud and clear on many occasions from the owner, the board, coaches and players.
“Any individuals that can’t summon the brain-power to comprehend this simple message and are found to have shamed the club by used using antisemitism or racist words or actions will face the strongest possible action from the club.”
Uefa is expected to rule on the complaints in a matter of days.
