A Greek Orthodox priest was shot and badly wounded on Saturday at a church in the French city of Lyon just days after a deadly terrorism attack on a church in Nice.

It was not immediately clear what the latest assailant’s motive had been, local authorities and prosecutors said.

The priest was fired on twice on Saturday afternoon as he was closing the church, and he was being treated for life-threatening injuries, a police source said.

Witnesses said the church, in the centre of the city, was Greek Orthodox. Another police source said the priest was of Greek nationality and had been able to tell emergency services as they arrived that he had not recognised his assailant.

A Greek government official identified the priest as Nikolaos Kakavelakis.

A suspect who fled the scene was arrested several hours later at a kebab shop in Lyon and placed in police custody, the first police source said. There was no confirmation the person was the suspected assailant, however, or if police were still looking for someone else.

There was no indication from French officials that the attack was terrorism-related.

A taped off area near the Orthodox Church where an attacker armed with a sawn-off shotgun wounded a priest in Lyon. Photo: Getty

The incident came two days after a man shouting “Allahu Akbar!” (God is Greatest) beheaded a woman and killed two other people in a church in Nice.

Two weeks ago, a schoolteacher in a Paris suburb was beheaded by an 18-year-old attacker who was apparently incensed by the teacher showing a cartoon of the Prophet Mohammad during a class.

Government ministers had warned there could be other Islamist militant attacks. President Emmanuel Macron has deployed thousands of soldiers to protect sites such as places of worship and schools.

The Nice attack took place on the day Muslims celebrate the Prophet Mohammad’s birthday. Many Muslims around the world have been angered about France’s defence of the right to publish cartoons depicting the prophet.

A third person has been taken into police custody in connection with that attack, a police source said on Saturday. The suspected assailant was shot by police and remained in critical condition in hospital.

Mr Macron took to Arabic-language airwaves on Saturday, telling Al Jazeera he understood the publication of cartoons depicting the Prophet Mohammad may shock some people but there was no justification for acts of violence.

The teacher killed on October 16, Samuel Paty, had showed cartoons in class to prompt discussion of free speech.