Pope Francis has warned against religious fanaticism and appealed for dialogue to battle violence during an open-air mass for Egypt's Catholic community.

The mass of peace on Saturday was attended by some 15,000 Egyptians and wrapped up a two-day visit by the Pope aimed at improving ties between Muslims and Christians.

"Peace be with you," the 80-year-old Francis said in Arabic as he started his homily at a heavily guarded military stadium in the capital, Cairo.

Continuing in Italian, he said: "True faith leads us to protect the rights of others with the same zeal and enthusiasm with which we defend our own."

He urged worshippers to be good and merciful to fellow Egyptians and said, "the only fanaticism believers can have is that of charity".

"Any other fanaticism does not come from God and is not pleasing to him."

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Francis' visit - coming after the Islamic State of Iraq and Levant (ISIL) killed dozens of worshippers in a series of Church bombings earlier this month - gave Egypt's embattled Christian community an occasion to be joyful.

It was the first visit by Francis to Cairo but the second by a Catholic pope.

The crowds arrived early for the mass, waving Egyptian and Vatican flags and braving intense security measures to welcome the Pope, who toured the sun-drenched stadium in a golf cart to the sound of hymns performed by a choir and orchestra.

Security was tight; helicopter gunships circled the perimeter of the stadium and armoured military vehicles patrolled the streets of Cairo.

It was, said Coptic Catholic engineer Maged Francis, a "historic occasion".

"It's unlikely it will ever happen again," he said. "Today joy has eclipsed the sadness of the last few weeks."

Manal George, who came from a middle-class neighbourhood in Cairo with her nephew to attend the mass, said the pope's visit brought much-needed cheer to Egypt's Christians.

"By coming to Egypt, the pope has taken away the sadness to replace it with joy," she said.

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ISIL has threatened more attacks against Egypt's Christians, who make up 10 percent of the 92 million population and constitute the largest Christian community in the Middle East.

Egypt's Catholic community is estimated at about 272,000, with much of the rest following the Coptic Orthodox Church.

On his first day, the pontiff urged Muslim leaders to renounce religious fanaticism that leads to violence. He made the appeal during a landmark visit to Cairo's Al-Azhar - the revered 1,000-year-old seat of Sunni Islam learning that trains clerics and scholars from around the world.

Recent assaults on churches - one in Cairo in December and twin Palm Sunday attacks in cities north of the Egyptian capital - have claimed at least 75 lives and wounded scores.

The attacks led to heightened security at churches nationwide and the declaration of a state of emergency by President Abdel Fattah el-Sisi.