Pope Francis said 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.
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 licences 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 licence 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 favour 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 neighbourhoods, 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 towards the love of God, toward maturity," he said.
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