"I am profoundly saddened, my thoughts go out to those who lost their lives in the attack in Brussels," the 77-year-old pontiff said as he arrived in Israel on the final leg of a three-day Middle East tour.
"I entrust the victims to God," he said of the attack which took place at the Jewish museum in the Belgian capital. The shooting also killed a French national and left a fourth person in critical condition.
The attack, which took place in central Brussels yesterday afternoon, drew condemnation from European leaders, and was blamed by Israeli Prime Minister Benjamin Netanyahu on a growing wave of anti-Semitism sweeping Europe.
Speaking at a formal ceremony at Ben Gurion airport near Tel Aviv after flying in from the West Bank city of Bethlehem, Francis reiterated calls for an end to anti-Semitism and intolerance.
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"Let us promote an education... Where there will be no place for anti-Semitism in any of its forms or for expressions of hostility, discrimination or intolerance towards any individual or people," he said.
He also spoke out against religious intolerance in an apparent reference to a wave of anti-Christian attacks by Jewish extremists ahead of his arrival in the Holy Land.
This morning, police arrested 26 Jewish extremists protesting at a site on Mount Zion where the pope will celebrate mass tomorrow.
Earlier this week, police imposed restraining orders on 15 extremists barring them from sites the pope will visit.