"Let no one consider themselves to be the 'armour' of God while planning and carrying out acts of violence and oppression," the pontiff said in speech at the presidential palace in Tirana.
"May no one use religion as a pretext for actions against human dignity and against fundamental rights."
The 77-year-old spiritual leader of the world's 1.2 billion Catholics made the declaration at the start of a packed one-day visit to majority-Muslim Albania, which he held up as an "inspiring example" of religious harmony.
But hundreds of thousands of Christians and Muslims thronging the Albanian capital to greet him.
Francis in his speech praised the "respect and mutual trust between Catholics, Orthodox (Christians) and Muslims" in Albania, which he called "a precious gift to the country".
He stressed that such coexistence was especially important "in these times where an authentic religious spirit is being perverted and where religious differences are being distorted and instrumentalized".
In a seeming reference to the Islamic State organisation, which espouses a radical and brutal interpretation of Islam to pursue a dream of reviving a caliphate in Syria and Iraq, as well as Nigeria's Boko Haram, the pope said the twisting of faith "created dangerous circumstances which led to conflict and violence".
The Vatican has voiced unusual support for US air strikes in Iraq to defend persecuted Christians there.
At the same time, though, the pope is spreading his message of interfaith tolerance around the world.
The Holy See hopes Albania -- a country with one of the youngest populations in Europe -- will be a vibrant source for converts in a continent gripped by secularism.
Yellow-and-white Vatican flags flew alongside Albanian ones in the main streets of the capital while vast portraits of Catholic priests and nuns persecuted under communism -- when Albania became the world's first atheist state -- were strung across roads.
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