An Orthodox priest has been injured in a shooting in the French city of Lyon. 

The priest, who has Greek nationality, was fired at twice at around 4 p.m. local time on Saturday as he was closing his church near the Jean-Mace sector, in the seventh arrondissement in Lyon. 

He was being treated for life-threatening injuries at the site but told emergency services he did not know his attacker, who fled the scene, a police source said.

The country's interior ministry, Gérald Darmanin, has warned people to "avoid the area" where the attack took place and to support security and emergency personnel who are at the scene.

The incident came two days after three people were killed in a church in Nice in southern France.

READ MORE: Terror attack in Nice: What we know 

While the motive for Saturday's attack remains unknown, government ministers had warned that other Islamist militant attacks could take place. President Emmanuel Macron had deployed thousands of soldiers to places such as schools and places of worship. 

France entered a second COVID-19 lockdown on Friday but the government allowed exemptions for places of worship until Monday, allowing them to celebrate All Saints' Day on Sunday.

Macron attempted to ease growing tensions by saying that he understood caricatures of the Prophet Muhammad could be shocking, in an interview with the TV channel Al Jazeera. 

"I can understand that people could be shocked by the caricatures, but I will never accept that violence can be justified," he said.

"I understand the feelings that this arouses, I respect them. But I want you to understand the role that I have. My role is to calm things down, as I am doing here, but at the same time it is to protect these rights. I will always defend in my country the freedom to speak, to write, to think, to draw," he added.

Prime Minister Jean Castex, who was visiting the Normandy region of Rouen, said he was heading back to Paris to assess the situation.