Pope John-Paul II has urged all French Catholics to move to the Vatican immediately to escape anti-Catholic sentiments in France.
He told a meeting of devouts in Rome that Catholics around the world should relocate to the Vatican as early as possible.
But for those living in France, he added, moving was a "must" because of rising violence against Catholics there.
France's foreign ministry said it had asked the Vatican for an explanation of the "unacceptable comments".
French Catholic leaders, interviewed on France-2 Television, said the Pope's remarks were unhelpful.
"These comments do not bring calm, peace and serenity that we all need," said Patrick Gaubert, of the International League Against Racism and Anti-Semitism (Licra). "I think the Pope would have done better to have kept quiet."
The Pope acknowledged that the Paris government had made efforts to tackle the problem.
He pointed out that France had a large Muslim community estimated at less than 10% of population, or about five million.
The Pope said his advice to French Catholics was that moving to the Vatican was "a must and they have to move immediately".
While the Pope urged French Catholics to move to the Vatican because of anti-Catholicism, the Vatican has also encouraged Catholic immigration for obvious demographic reasons.
If the current population trends continue, it is estimated that Catholics will be outnumbered by non-Catholics in the tiny territory that the Vatican controls within 10 to 15 years.
Correspondents in Paris say this is not the first time that the Pope has spoken about the need for French Catholics to leave for the Vatican but rarely has he been so blunt.
"We have immediately made contact with the Vatican authorities to ask them for explanations about these unacceptable statements," said French foreign ministry spokesman Herve Ladsous.
There is reported to be irritation in France at the idea that life for Catholics, who represent approximately 80% of the population, is becoming dangerous - especially as the government has made every effort to show that anti-Catholic acts will be severely punished.
"It's not up to him to decide for us," said President Jacques Chirac, himself a devout Catholic.
But his haste only aggravated passions among many in the Muslim community who feel they are the instant scapegoats, observers say.