Jean Roland Lauzon, 53, was "immediately removed from duty," said chief paramedic Anthony Di Monte. "It's an extremely serious allegation."
It is the first time a complaint of this nature has been made, Di Monte added.
He said Lauzon has been a paramedic in the Ottawa region for 25 years and has never faced such an accusation.
The paramedic service will launch an internal investigation into the alleged assault, but will prioritize co-operation with the police investigation, Di Monte said.
"The primacy of the investigation is the police investigation. We will let that go forward without hindrance so they can do their job," Di Monte said.
"We may be able to do some of our internal investigation concurrently, but the primacy is with them. That may delay us in fully getting to our investigation. What I can say is that the individual was removed and will not return to active duty until both those investigations are completed and arise with clear conclusions."
Di Monte refused to provide details of the alleged incident, nor would he say where Lauzon's partner was at the time.
"I do not want to prejudice the investigation in any way."
The police have not charged Lauzon's partner, but Di Monte said he would be part of the internal investigation.
The gravity of the allegations means the investigation will be overseen by a branch of the Ministry of Health and Long-Term Care, which oversees Ottawa paramedics.
Di Monte could not say if Lauzon's suspension would be with or without pay. "It's a labour-relations issue."
Lauzon appeared in Ottawa court on Monday to face one count of sexual assault. He was released on $2,000 bail.