The Portugal forward was struck on the head by what was thought to be a lighter as the players left the field for half-time after he had scored two penalties in Real Madrid's 2-0 Copa del Rey semi-final win at Vicente Caldern on Tuesday.
The win gave Real a 5-0 aggregate victory, but goalkeeper Casillas was left with a sour taste in the mouth.
"There is always someone that tries to smear the image of a club like Atletico Madrid and it doesn't reflect how the majority of their fans are," he told Real's official website.
"I think the consequences could be serious, because it could have hurt a player."
The incident follows reports of racist chants directed at Real left-back Marcelo by Atletico fans after the opening leg.
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