An attacker armed with a sawn-off shotgun seriously wounded a Greek Orthodox priest in a shooting outside a church in the French city of Lyon on Saturday, with the country still reeling from a deadly church attack days before.

Nikolaos Kakavelaki, 52, was closing his Lyon church mid-afternoon when he was attacked and is now in a serious condition in hospital, said a police source who asked not to be named.

The attacker fled the scene but Lyon's public prosecutor later announced that a suspect had been arrested.

"A person who could correspond to the description given by the initial witnesses has been placed in policy custody," prosecutor Nicolas Jacquet said, adding that the suspect had not been carrying a weapon when he was arrested.

The priest was shot twice in the chest at point-blank range, according to sources close to the inquiry.

The motive for the attack was not clear.

"At this stage, no hypothesis is being ruled out, nor favoured," Jacquet said.

But it comes at a time when France is already on edge after the killing of three people inside a church in Nice on Thursday and the beheading of a teacher earlier this month who had showed his class a cartoon of the prophet Mohammed.

The Lyon prosecutor's office said in a statement that witnesses, and a passing police patrol, heard gunshots then "saw an individual fleeing and discovered a man with gunshot wounds at the back door of the church".

The prosecutors said that an investigation had been launched, and it remains "in close contact with the national anti-terrorist prosecution".

The small, art-deco style Orthodox church is situated in a residential area of Lyon which was especially quiet due to the new lockdown measures introduced in France on Friday to stem the growing coronavirus pandemic.

In Paris, Interior Minister Gerald Darmanin opened a crisis cell meeting to consider the situation.

Archbishop Ieronymos, the head of the Greek Orthodox church, denounced a "horror that defies human logic".

"Intolerant and fanatic extremists, fundamentalists of violence and death use religion as a bullet which aims at the heart of freedom and especially the freedom of belief of others," he told reporters in Athens.

European Council President Charles Michel condemned "this new abominable act in Lyon".

He added in a tweet that "in Europe, the freedom of conscience is guaranteed for all and must be respected, violence is intolerable and must be condemned".

EU Parliament President David Sassoli said that "Europe will never bow to violence and terrorism".

Saturday's shooting comes after three people were killed in a knife rampage inside a church in the southern town of Nice on Thursday.

A Tunisian suspect was shot and injured by police near the scene of that attack.

France was already tense after the republication in early September of cartoons of the prophet Mohammed by the satirical Charlie Hebdo magazine, which was followed by an attack outside its former offices, the beheading of the teacher and the attack in Nice.

After the teacher's death, President Emmanuel Macron said France would never renounce its laws permitting blasphemous caricatures, sparking protests across the Muslim world.

In an apparent bid to reach out to Muslims, Macron gave an interview with Qatar-based TV channel Al-Jazeera on Saturday in which he said he understood that caricatures of Mohammed could be shocking.

He also lashed out at "lies" that the French state was behind the caricatures, and said he will "always defend in my country the freedom to speak, to write, to think, to draw".

Foreign Minister Jean-Yves Le Drian has warned that French citizens face a security risk "wherever they are", saying alerts had been sent to all French nationals abroad.

Prime Minister Jean Castex spoke of "the government's determination to allow each and everyone to practice their worship in complete safety and in complete freedom."

He was speaking in the northwestern town of Saint-Etienne-du-Rouvray, where a catholic priest was killed in an Islamist attack in 2016.

France went into a second coronavirus lockdown on Friday but the government has exempted places of worship until Monday, allowing them to celebrate the Christian All Saints' Day on Sunday. (AFP)

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