The pontiff in a criticism of the controversial real- estate tycoon had said that Trump cannot claim to be a Christian and slammed his comments on immigration in particular building a wall along the US-Mexico border.
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Trump, 69, in a swift reaction had fired back at the Pope calling Francis's remarks "disgraceful" but later softened his stand on the Catholic leader.
"I don't like fighting with the Pope, actually. I don't think this is a fight. I think he said something much softer than was originally reported by the media. I think that he heard one side of the story, which is probably by the Mexican government," Trump said.
"I have a lot of respect for the Pope. I think he's got a lot of personality. He's a very different kind of a guy, and I think he's doing a very good job. He's a lot of energy," Trump said at a townhall organised by CNN in South Carolina.
Pope's comment had come in an interaction with reporters travelling on his plane on his way back to Vatican from Mexico where he visited this week.
"A person who thinks only about building walls, wherever they may be, and not building bridges, is not Christian," Pope Francis had told reporters.
"Thank God he said I was a politician, because Aristotle defined the human person as 'animal politicus.' So at least I am a human person. As to whether I am a pawn - well, maybe, I don't know. I'll leave that up to your judgment and that of the people," said the 79-year-old leader of 1.2 billion Catholics.
Trump late last night said: "I would say that I think he was very much misinterpreted, and I also think he was given false information. If he would have heard our side from people that live in the United States?"
But earlier in the day he had called Pope's comment "disgraceful."
"For a religious leader to question a person's faith is disgraceful. I am proud to be a Christian and as President I will not allow Christianity to be consistently attacked and weakened, unlike what is happening now, with our current President," Trump had said.
He said he was surprised to see the comment from the Pope.
"I didn't think it was a good thing for him to say, frankly. He was talking about the border. I'm very strong on border security. We are talking about building a wall. We're gonna build a wall, and Mexico's gonna pay for the wall, and that's the way it is," Trump had said.
Trump's rivals from his own Republican party supported him and differed with Francis in separating religion and politics.
"I just don't think it's appropriate to question Donald Trump's faith. He knows what his faith is. And if he has a relationship with the lord, fantastic. If he doesn't, it's none of my business," former Florida Governor Jeb Bush, a Catholic, said.
"We have a right to build a wall, but I've got to tell you, there are too many walls between us. We need bridges between us if we're going to fix the problems in Washington because all they do is have walls," Ohio Governor John Kasich said.
Florida Senator Marco Rubio, a devout Catholic, said he disagreed with Francis.
"I disagree with a lot of thing that Donald Trump has said, but I do think America has right to secure its border," he told Fox News.
Rubio stressed that America is "one of the most generous countries" in the world when it comes to immigration.
"We admit a million people every year permanently legally to this country. Mexico does not do that, other countries do not do that," he said.
The White House refrained from entering into the controversy but took a dig at Trump.
"I think I can just say, as a general matter, that President Obama had the opportunity a couple of weeks ago to address the National Prayer Breakfast, where he talked about his own personal faith, his own personal Christian faith, informed his view of the values and priorities that he has chosen to champion in the White House," White House Press Secretary Josh Earnest said.
"We have noted, I think on a number of occasions, we've had the opportunity to note that many of those values and priorities are not shared by Trump. So I will, however, though, extend to Trump the courtesy that he has not extended to the President, and not use this opportunity to call into question the kind of private personal conversations that he's having with his God," Earnest said.
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