He made headlines after giving a speech during the church festival "Holy Name of Mary", which was first introduced 333 years ago in gratitude for the victory over the Ottomans in the famous Battle of Vienna in 1683.
According to the Archdiocese of Vienna, the cardinal said: "Will there now be a third attempt at an Islamic conquest of Europe? Many Muslims long for it and say: Europe is at the end."
However, in an update posted on the Archdiocese's website he said his words had been misinterpreted on social media as an attack against Muslims and refugees.
“One must not take my homily to be a call to defend ourselves against the refugees, this was not at all my intention,” he said.
He added that he believes Europe's Christian heritage was “in danger,” but it was a self-inflicted problem and has “absolutely nothing to do with Islam or 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.”
The Pope has repeatedly urged that people have greater empathy and compassion for the thousands of refugees and migrants arriving in Europe from the Middle East and Africa.
Cardinal Schönborn has often been listed as one of the most likely candidates to take over the position of Pope, although in previous elections he was deemed too young.