The orthodox priest was shot as he was closing his church at around 4pm local time.
He is being treated for life threatening injuries, while the suspect is on the run.
The incident comes after three people were stabbed to death in a church in Nice earlier this week in a suspected terror attack.
French President Emmanuel Macron has deployed thousands of soldiers to protect sites such as places of worship and schools in response to the knifings at the Notre Dame church on Thursday.
France is on high alert for terror attacks amid controversy over cartoons of the Prophet Mohammed.
Earlier this month, a teacher was beheaded in Paris after showing caricatures of the Prophet Mohammed for a class on free speech.
More to follow…