The SIU said the incident happened May 1 this year at the Queensway-Carleton Hospital.
The alleged victim, 32-year-old Ismael Awaleh, was in police custody at the hospital at the time and suffered an injury, the SIU said.
Ottawa police constables Erin Cavan and Jordan Blonde are each facing one count of assault. They are expected to appear in an Ottawa courtroom on Dec. 16.
Both officers remain on active duty, an Ottawa police spokesperson said Monday.
Awaleh facing 7 criminal charges
According to court documents, Awaleh is alleged to have assaulted a woman and breached a probation order on April 29.
Then, two days later on May 1, it's alleged that Awaleh was found to be in possession of crack cocaine, and that he assaulted Blonde and resisted Blonde and Cavan's attempts to arrest him.
He's facing seven charges in total, including one count of drug possession, two counts of resisting arrest, two counts of assault and two counts of breaching probation.
Awaleh's criminal record, which dates back to 2008, includes prior convictions on drug possession and breaching probation.
The SIU is an independent agency that investigates incidents of death, serious injury or allegations of sexual assault involving police.