Pope Francis on Wednesday suggested that Donald J. Trump “is not Christian” because of the harshness of his campaign promises to deport more immigrants and force Mexico to pay for a wall along the border, New York Times reported.

“A person who thinks only about building walls, wherever they may be, and not building bridges, is not Christian,” Francis said when a reporter asked him about Mr. Trump on the papal airliner as he returned to Rome after his six-day visit to Mexico.

Asked whether he would try to influence Catholics in how they vote in the presidential election, Francis said he “was not going to get involved in that” but then repeated his criticism of Mr. Trump, with a caveat.

“I say only that this man is not Christian if he has said things like that,” Francis said. “We must see if he said things in that way and in this I give the benefit of the doubt.”

Mr. Trump responded immediately at a campaign rally in Kiawah Island, S.C. Discussing the Islamic State, “their primary goal is to get to the Vatican.”

“If and when the Vatican is attacked,” he said, “the pope would only wish and have prayed that Donald Trump would have been elected president.”

Earlier in his remarks, he said, “I like the pope.”

Asked about the comments, Francis laughed. “Thank God he said I was a politician because Aristotle defined the human person as ‘animal politicus,’ ” he said.

“So at least I am a human person,” the pope said. “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.”

Francis also took questions on a handful of other issues.

Donald J. Trump said it was “disgraceful” that Pope Francis questioned his faith on Thursday and suggested that his presidency would be the answer to the Vatican’s prayers because he would protect it from terrorists if elected.

As he returned to Rome after his six-day visit to Mexico, Francis said, “A person who thinks only about building walls, wherever they may be, and not building bridges, is not Christian,” in response to a question about Mr. Trump aboard the papal airliner.

Mr. Trump condemned that remark during a campaign rally in South Carolina, describing himself as a good Christian and arguing that Francis does not understand America’s immigration crisis.

“For a religious leader to question a person’s faith is disgraceful,” Mr. Trump said.

The Trump campaign also released a statement from the candidate, defending his hard-line policies on immigration and saying the pope was out of line.

“No leader, especially a religious leader, should have the right to question another man’s religion or faith,” Mr. Trump said, going on to claim that the pope was being used for political purposes by the Mexican government. “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.”

Mr. Trump went on to say that he would defend Christianity more aggressively than current political leaders.

“If and when the Vatican is attacked by ISIS, which as everyone knows is ISIS’ 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,” Mr. Trump said.

Other members of Mr. Trump’s campaign also pushed back against the pope. Dan Scavino, his social media director, posted an image of Vatican City and noted that it is surrounded by a wall.

And Jerry Falwell Jr., the president of Liberty University and a supporter of Mr. Trump, said that the pope had crossed a line.

“Jesus never intended to give instructions to political leaders on how to run a country,” Mr. Falwell told CNN.

The Pope also made a distinction between abortion and birth control. He flatly ruled out condoning abortion, which he described as “a crime, an absolute evil.” But he seemed more open to making an exception for contraception, citing Pope Paul VI’s decision in the 1960s to make an emergency exception and permit nuns in the Belgian Congo to use contraceptives because they were in danger of rape.

“Avoiding pregnancy is not an absolute evil,” Francis said. “In certain cases, as in this one, as in that one I mentioned of Blessed Paul VI, it was clear. I would also urge doctors to do their utmost to find vaccines against these mosquitoes that carry this disease.”

Francis’ comments on Mr. Trump and the possibility of using contraceptives to prevent the spread of the Zika virus are certain to garner strong reactions. The church has long opposed the use of artificial contraceptives, a ban reaffirmed by Paul VI in his 1968 papal encyclical, Humanae Vitae.

Francis made his remarks about Mr. Trump barely three hours after he had concluded his Mexico trip by presiding over a huge Mass in the border city of Ciudad Juárez. He first walked to the edge of the Rio Grande — as American security officers watched from the other side — to lay flowers at a new memorial commemorating those who have died trying to cross the border.

Francis then celebrated Mass, as a crowd of more than 200,000 people stood barely a stone’s throw from the border and listened to the pope call for compassion for immigrants fleeing chaos, poverty and war.

Mr. Trump has staked out controversial positions on immigration, vowing to force Mexico to build a wall and also increase deportations. He has also made inflammatory comments accusing Mexican immigrants of being rapists and criminals.

In the days before Francis arrived at the border, Mr. Trump criticized the visit, calling the pope a political person and accusing him of acting at the behest of the Mexican government. “I think that the pope is a very political person,” he said.

Mr. Trump, in an interview with Fox Business Network, said: “I don’t think he understands the danger of the open border that we have with Mexico. I think Mexico got him to do it because they want to keep the border just the way it is. They’re making a fortune, and we’re losing.”

Mr. Trump is a Presbyterian and has been trying to make inroads among evangelical voters as he seeks to win the coming set of Southern primaries.

Francis was asked about recent reports about newly disclosed letters revealing the closeness of the relationship between Pope John Paul II and Anna-Teresa Tymieniecka, a philosopher and author who collaborated with John Paul. Francis argued that a close friendship between a man and woman “is not a sin, it’s a friendship. A romantic relationship with a woman who is not your wife — that is a sin. Understand?”

He said that popes were men but that they needed advice and friendship from women. Such relationships need not stir suspicions, he said. “The pope, too, has a heart that can have a healthy, holy friendship with a woman,” he said.

Asked about the continuing problem of clerical sexual abuse, Francis defended his record despite criticism that he is not sufficiently focused on the issue. He listed the things he has done to speed up prosecution of cases in the Vatican’s judicial system, but agreed that “we need to work faster, because we’re behind with the cases.”