Hundreds of mourners have attended Rouen Cathedral in northern France for the funeral of the elderly Roman Catholic priest killed at a church altar by two Islamist militants.

Father Jacques Hamel was leading morning mass in the nearby industrial town of Saint-Etienne-du-Rouvray last Tuesday when the attackers stormed in, forced the 85-year-old to his knees and slit his throat while chanting in Arabic.

A long procession of clergy, bishops and archbishops followed four pallbearers, who carried Fr Hamel's coffin into the 13th Century gothic Cathedral through the "Door of Mercy" and placed it on an ornate rug before the altar.

Addressing the congregation, his sister Roselyne Hamel recounted how during his military service in Algeria her brother had refused an officer's grade so as not give the order to kill others, and how he once emerged the sole survivor in a desert shootout.

People watch Fr Hamel's funeral on a giant screen outside Rouen's cathedral

"He would often ask himself why me? Today, Jacques, our brother, your brother, you have your answer: Our God of love and mercy chose you to be at the service of others," she said.

The service, which took place amid tight security, was to be followed by a private burial.

Fr Hamel became the latest victim of a terror attack in France when two 19-year-old jihadists murdered him at the altar.

Abdel Malik Petitjean and Adel Kermiche had pledged allegiance to the so-called Islamic State group and both were shot dead by police.

One person in the church was seriously wounded during the attack and three others escaped unharmed.

The attack stunned France's religious communities, sparking fears of tensions in a country with a population of about five million Muslims.

A person holds a picture of the priest Jacques Hamel outside Rouen's cathedral

However, the two communities have largely rallied together, with churches opening their doors to Muslims on Sunday for a moving tribute to Fr Hamel, and against radical Islam.

Pope Francis said Islam could not be equated with terrorism.

"It's not true and it's not correct (to say) Islam is terrorism," he said, defending his decision not to name Islam when condemning the brutal murder.

"If I have to talk about Islamic violence I have to talk about Christian violence. Every day in the newspapers I see violence in Italy, someone kills his girlfriend, another kills his mother-in-law, and these are baptised Catholics."

The church attack came just two weeks after Tunisian Mohamed Lahouaiej Bouhlel ploughed a 19-tonne truck into a massive crowd celebrating Bastille Day in the Riviera city of Nice, leaving 84 dead and injuring more than 300 people.

The repeat attacks in France have raised tough questions about security failures, but also about the foreign funding of many mosques.

Interior Minister Bernard Cazeneuve said yesterday that authorities have shut down around 20 mosques and prayer halls considered to be preaching radical Islam since December.

"There is no place ... in France for those who call for and incite hatred in prayer halls or in mosques, and who don't respect certain republican principles, notably equality between men and women," the minister said.