An attacker armed with a sawn-off shotgun on Saturday wounded an Orthodox priest in a shooting in the French city of Lyon before fleeing, said a police source.

The 52-year-old priest, who has Greek nationality, was closing his church mid-afternoon when the attack happened and is now in a serious condition in hospital, said the source, who asked not to be named.

The attack comes at a time when France is already on edge over the killing of three people inside a church and the beheading of a teacher who showed a class a cartoon of the prophet Mohammed.

The priest was shot in the liver at point-blank range, according to sources close to the enquiry.

No weapon was found at the scene of the shooting. The interior ministry tweeted that "an incident is underway" in the southeastern city of Lyon.

"Security and emergency personnel are at the scene," the ministry added, warning people to "avoid the area" where the attack took place. The search for the assailant was underway.

The small 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.

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."

Security and emergency personnel at the scene of the attack in Lyon on Saturday
Security and emergency personnel at the scene of the attack in Lyon on Saturday AFP / PHILIPPE DESMAZES

The shooting comes just days after three people were killed in a knife rampage inside a church in the southern town of Nice.

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

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

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.

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.

France has been on high alert since the January 2015 massacre at Charlie Hebdo marked the beginning of a wave of jihadist attacks that have killed more than 250 people.

Tensions have heightened since last month, when the trial opened for 14 suspected accomplices in that attack.

After the deadly attack in Nice, President Emmanuel Macron announced increased surveillance of churches by France's on-the-street military force, which is to be bolstered to 7,000 troops from 3,000.

Security at schools will also be boosted, he said. Schools are remaining open during the new lockdown.