Pope Francis said on Monday government officials have a "human right" to refuse to discharge a duty, such as issuing marriage licenses to homosexuals, if they feel it violates their conscience.
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Speaking to reporters as he returned home from a 10-day trip to the United States and Cuba, Francis also repeated his condemnation of priests who had sexually abused children, saying the victims had been "crushed by evil."
Although the Argentine-born pontiff delved into some of the United States' thorniest political debates during his visit, he never specifically referred to a controversy over same-sex marriages, which the Church firmly opposes.
On the flight back to Rome, he was asked if he supported individuals, including government officials, who refuse to abide by some laws, such as issuing marriage licenses to gays.
"Conscientious objection must enter into every juridical structure because it is a right," Francis said.
Earlier this month a county official in the state of Kentucky, Kim Davis, went to jail because she refused to issue a marriage license to a gay couple following a Supreme Court decision to make homosexual marriage legal.
Davis's case has taken on national significance in the 2016 presidential campaign, with one Republican contender, Mike Huckabee, holding rallies in favor of Davis, a Apostolic Christian, who has since joined the Republican party.
"I can't have in mind all cases that can exist about conscientious objection but, yes, I can say that conscientious objection is a right that is a part of every human right," he said, speaking in Italian.
"And if someone does not allow others to be a conscientious objector, he denies a right," he added.
Francis said conscientious objection had to be respected in legal structures. "Otherwise we would end up in a situation where we select what is a right, saying: 'This right has merit, this one does not.'"
In the hour-long, freewheeling talk that has become a trademark of his papacy, the pope returned to the problem of priestly abuse. On Sunday, he met five victims of sexual abuse and issued his most comprehensive condemnation of the crime.
On the plane, Francis said sexual abuse was not confined to the Church but it was worse when committed by men of religion.
"We know abuses are everywhere, in families, in the neighborhoods, in the schools, in the gyms, but when a priest abuses it is very grave because the vocation of the priest is to make that boy, that girl grow toward the love of God, toward maturity," he said.
"But instead (the victim) is crushed by evil and this is nearly a sacrilege because the priest has betrayed his vocation, the calling of the Lord," the pope said.
The pope had been fiercely criticized by abuse victims on Wednesday, after he initially addressed the scandal but did not utter the words "sexual abuse", and praised American bishops for their handling of the crisis.
Asked about barriers being but up in Europe to stop the influx of migrants, the pope said: "All walls collapse, today, tomorrow or after 100 years, but they will collapse. Walls are not a solution."
He said that while it was true that Europe was struggling in the face of a refugee crisis, the solution had to be found through dialogue. "Barriers last a short time or a long time, but the problem remains and with it, more hatred."
A reporter said the pope had become a "star" in the United States following his visit to Washington, New York and Philadelphia, and asked if this was good for the Church.
"The media uses this term, but there is another truth - how many stars have we seen go out and fall. It is a fleeting thing. Instead being a 'servant of the servants of God' does not pass," the pope said, referring to one of the titles of his office.