"The Pope's expression is in no way intended to be interpreted as a justification for the violence and terror that took place in Paris last week," said a statement from Vatican spokesman Fr. Thomas Rosica.
Speaking to journalists as he flew from Sri Lanka to the Philippines, the Pope condemned the Jan. 7 terrorist attack on the French satirical weekly Charlie Hebdo but warned there were limits on freedom of expression.
He called freedom of expression a "fundamental human right" and stressed that killing in the name of God was an unacceptable "aberration."
"You don't kill in God's name," Francis said. However the Pope, who has made a point of reaching out to Muslims, Jews and other faiths, said there were limits to self-expression when it involved insulting or ridiculing people's faith.
"You cannot provoke, you cannot insult the faith of others," he said. "You cannot make fun of the faith of others."
By way of example, the Pope referred to Alberto Gasparri, who organizes the papal trips and was beside him on the plane.
He said if Gasparri cursed the Pope's mother, he could "expect a punch," and at that point he gestured with a fake punch towards Gasparri, saying: "It's normal. You cannot provoke. You cannot insult the faith of others.
You cannot make fun of the faith of others."
Those words prompted the Vatican clarification. "The Pope's words about Dr. Gasbarri were spoken colloquially and in a friendly, intimate matter among colleagues and friends on the journey," said the statement.
"His words mean that there are limits to humour and satire, particularly in the ways that we speak about matters of faith and belief. "Pope Francis' response might be similar to something each of us has felt when those dearest to us are insulted or harmed. The Pope's free style of speech, especially in situations like the press conference, must be taken at face value and not distorted or manipulated.
"The Pope has spoken out clearly against the terror and violence that occurred in Paris and in other parts of the world. . . Pope Francis has not advocated violence with his words on the flight."
Freedom of expression has remained a hotly contested issue since Islamist terrorists stormed the office of the weekly known for mocking Islam, Judaism and Christianity.
Several cartoonists were killed in the first of three days of terror attacks that rocked France and claimed the lives of 17 victims and three terrorists.
On Jan. 8, four French imams on a visit to the Vatican issued a statement denouncing the violence and appealing to people whatever their faith to do more to promote a "culture of peace and hope."
(With files from Religion News Service)