He had said in a speech to mark the 333rd anniversary of the Battle of Vienna: "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."
The Cardinal reportedly went on to pray: "God have mercy on Europe and on thy people, who are in danger of forfeiting our Christian heritage". He added that this was already being felt "not only economically, but above all, in human and religious matters".
However, his office insists that he was "not championing a sort of defensive battle, defending Christian values against Islam".
The Cardinal has offered a clarification: "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."
He continued: "One must not take my homily to be a call to defend ourselves against the refugees, this was not at all my intention. The opportunity for a Christian renewal of Europe lies in our hands: if we look at and come to Christ, spread his gospel and deal with our fellow men, strangers included, as he has taught us, in love and responsibility."
Cardinal Schönborn, 71, is a conservative who has been referred to as the "spiritual son" of his one-time mentor, Pope Benedict XVI.
The comments came as a new study in the US found that only 14 per cent of Catholics have a favourable view of Muslims.