The Archbishop of Vienna, Cardinal Christoph Schönborn, had released a statement urgently asking Europeans not to lose their Christian heritage.
His office says his comments were "misinterpreted on social media as an attack against Muslims and even as directed against the refugees."
Cardinal Schonborn's words come after a speech earlier in the month when the Catholic leader said: "Islamists are not at fault for our weakness, but they can take advantage of it.
"Hope lies in returning to Christ, the gospel and works of charity."
He said he worried about the loss of Europe's Christian heritage during a recent homily in St Stephen's Cathedral.
The archbishop asked those gathered: "Will there be a third Islamic attempt to conquer Europe?
"Many Muslims think this and wish this and say that Europe is at its end."
His office says these words are not a direct attack on Islam or on Muslim refugees seeking safety in Europe.
Cardinal Christoph Schönborn asked God: "Do not abandon us, because we have become so mediocre in our faith."
The Cardinal concluded: "Europe's Christian legacy is in danger, because we Europeans have squandered it.
"That has absolutely nothing to do with Islam nor with the refugees.
"It is clear that many Islamists would like to take advantage of our weakness, but they are not responsible for it. We are."
