Khdeir is the cousin of Mohammed Abu Khedair, the 16-year-old burned alive in what is suspected to be an act of vengeance for the kidnapping and murders of three Israeli teenagers.
Khdeir's family showed pictures revealing his bruised and broken face. Israeli police say Khdeir attacked them during the protests before his cousin's funeral. They also said the video was doctored to misrepresent the events that took place.
Khdeir was visited in custody by an official from the American consulate on Saturday.
"We are profoundly troubled by reports that he was severely beaten while in police custody and strongly condemn any excessive use of force," said State Department spokeswoman Jen Psaki. "We are calling for a speedy, transparent and credible investigation and full accountability for any excessive use of force."