Pope Francis has expressed his "pain and horror" for another act of "absurd violence" after an elderly Catholic priest was murdered in northern France on Tuesday, having earlier being taken hostage along with parishioners.

Fr Jacques Hamel, 85, reportedly had his throat cut after two men armed with knives entered the church at Saint-Etienne-du-Rouvray, a suburb of Rouen, as mass was ending at about 9.30am on Tuesday. Two nuns and two other worshippers were held hostage and there are reports one of them was critically injured before the two attackers were shot dead by police.

The priest was described as a popular, courageous and dedicated man who had served people for most of his life.

Vatican spokesman Fr Federico Lombardi said the Pope has expressed his condemnation for "every form of hatred" and would be praying for all involved.

"We are particularly stricken because this horrible violence occurred in a church - a sacred place in which the love of God is proclaimed - with the barbaric killing of a priest," he said.

The so-called Islamic State claimed responsibility for the attack which French President Francois Hollande reportedly described as an "odious assassination".

Rev Dr Hielke Wolters, acting general secretary of the World Council of Churches, said the WCC community joined the grief of the people of France and the community of Saint-Etienne-du-Rouvray for this latest eruption of violence.

"It is particularly distressing when worshippers and professed religious are singled out, because their lives are put at the service of all," he said in a statement. "Yet it makes our resolve even stronger to stem violence at its very root by reaching out all the more to all people with an all-encompassing message of peace, justice, and nonviolence.”

Rev Dr Wolters also spoke out in the wake of an attack on a care centre for the mentally disabled in Japan in which 19 people were killed and more than 20 more injured. 

“All persons bear the image of God, are beloved of God, and deserve our loving care because, in the end, all persons are vulnerable. This assault violates our deepest convictions and the singular duty we owe each other as children of God,” he said.