A second hostage was in critical condition.
A priest, two sisters from a local order and two churchgoers were among those held.
Footage from the scene shows emergency crews arriving at the scene and one person being stretchered into an ambulance.
The two men rushed into the church during a morning service, soon after 9am.
"Two men armed with knives entered the church by the back entrance, and have taken five hostages," said a local police source.
A source said a third third nun had escaped and raised the alarm. Saint-Etienne du Rouvray has a population of 30,000 and is around seven miles from Rouen.
- Daily Mail and AFP