Bridging divisions between Muslims and Christians is a main theme of his first tour of the continent that also takes him to Uganda, which like Kenya has been victim of militant attacks, and the Central African Republic, riven by sectarian conflict.
"All too often, young people are being radicalised in the name of religion to sow discord and fear, and to tear at the very fabric of our societies," the pope told Muslim and other religious leaders gathered in the Kenyan capital Nairobi.
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"Ecumenical and inter-religious dialogue is not a luxury. It is not something extra or optional, but essential," he said at a morning meeting with about 25 religious leaders in the Vatican embassy here.
He stressed that God's name "must never be used to justify hatred and violence."
He referred to Somalia's al Shabaab terroists' 2013 attack on Nairobi's Westgate shopping mall and this year's assault on Marissa university. Hundreds of people have been killed in the past two years or so, with Christians sometimes singled out by the gunmen behind the raids.
The chairman of the Supreme Council of Kenya Muslims (Supreme), Abdullah El Busaidy, also called for cooperation and tolerance.
"As people of one God and of this world we must stand up and in unison, clasp hands together in all the things that are essential for our collective progress," he said at the meeting, adding doctrinal differences should be put aside.
The pope's tour will also seek to address the continent's fast-growing Catholic population, with the number of African Catholics expected to reach half a billion by 2050.
A third of Kenya's 45 million people are Catholics and tens of thousands of them gathered in pouring rain to attend the pope's open-air Mass in central Nairobi later on Thursday.
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"I am hoping that the pope is going to talk to young people and tell them especially to spread the word of peace and also give us hope," said 24-year-old Purity Wanjiku, who was standing amidst a sea of people sheltering under umbrellas.
Wanjiku was from Nairobi, but others had travelled from across the country, like Mark Odimo from the port city of Mombasa who simply said: "My aim is to see the pope."
Thousands of police officers, some mounted on horses, were deployed in Nairobi to protect the pope and control the crowds. Uganda, where al Shabaab carried out attacks in 2010, has also promised tight security.
The most hazardous stop may be the Central African Republic, where dozens of people have been killed since September in violence between mostly Muslim Selena rebels and Christian anti-balaka militias. The pope has brushed off safety concerns.
Later on Thursday, the pope visits the regional UN headquarters in Nairobi, where he is expected to address climate issues.
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