"Anyone, whoever he is, who only wants to build walls and not bridges is not a Christian," the pontiff told journalists during his return journey from a trip to Mexico.
He was responding to a question about the Republican White House hopeful's anti-immigrant stance.
"Vote, don't vote, I won't meddle. But I simply say, if he says these things, this man is not a Christian," Francis said.
"We need to see if he really said them and for this I will give him the benefit of the doubt."
Despite that qualifier, Francis's remarks drew swift and angry condemnation from the billionaire tycoon.
"For a religious leader to question a person's faith is disgraceful," Trump said in a statement delivered on a campaign stop in South Carolina, which holds its Republican primary this weekend.
"I am proud to be a Christian and as president I will not allow Christianity to be consistently attacked and weakened."
Trump has gained popularity by claiming Mexico is sending criminals to the United States, and last week he accused the pope of visiting the border between the two countries at the bidding of the Mexican government.
Francis was speaking after concluding a five-day trip to Mexico, where he delivered a mass before 300,000 people near the US border and decried the "human tragedy" of migrants fleeing violence worldwide.
In a highly symbolic gesture, the pontiff climbed a ramp facing the Rio Grande and looked out across the border into US territory, where hundreds of migrants waved at him.
Trump has vowed to build a wall on the US southern border to keep migrants from illegally crossing into the United States, a pledge that has caused a firestorm in the presidential campaign where immigration is a hot-button issue.
His reaction to the pope's comments was scathing.
"If and when the Vatican is attacked by ISIS, which as everyone knows is ISIS's ultimate trophy, I can promise you that the pope would have only wished and prayed that Donald Trump would have been president because this would not have happened," Trump said.
'Pope used as pawn'
Propagandists for ISIS -- one of several names for the Islamic State extremist group which controls swathes of Syria and Iraq -- have issued threats that their fighters will plant their flag on the top of St Peter's basilica.
But Italian officials have insisted they have no knowledge of any credible threat to the Vatican or the pope.
Trump said Mexican authorities had told the pope only "one side of the story."
"He didn't see the crime, the drug trafficking and the negative economic impact the current policies have on the United States.
"They are using the Pope as a pawn and they should be ashamed of themselves for doing so, especially when so many lives are involved and when illegal immigration is so rampant."
It was not the first time Trump had issued the pawn jibe, and Francis was asked about it on the plane.
"Am I a pawn of the Mexican government? I leave that to your judgement, to the people to judge," he said.
The 79-year-old Argentinian, a fervent critic of the freewheeling capitalism espoused by Trump, also said he was proud to have been branded a politicized pontiff by the tycoon.
"Thanks be to God if that is what he said, because Aristotle defined man as a political animal: at least (it means) I am a human person."
Trump has promised to end illegal immigration by building a wall along the Mexican border, which stretches more than 3,100 kilometerss (1,950 miles) -- a third of it currently covered by high-security fencing.
Trump's verbal clash with the pope was just the latest, dramatic illustration of his brash, confrontational brand of politics that has upended the 2016 White House race.
It was unclear what, if any, impact the incident could have on his electoral chances.
One of Trump's Republican rivals, former Florida governor Jeb Bush, who has clashed bitterly with the billionaire businessman, was charitable toward him in remarks Thursday addressing the contretemps.
"I don't question anybody's Christianity, because I honestly believe that's a relationship you have with your creator," Bush, a devout Catholic, told reporters.
"I support walls and fencing where it's appropriate for sure. I also believe we ought to have other parts of this. The border patrol. Using drone technology. Using GPS technology -- a strategy to protect our border. That is clear," he said.
"That's not an un-Christian thing to do, to make sure people don't come across our border illegally. That's a just thing to do."
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