"To attack the Pope because he referred to a historical document in a speech is fully unacceptable," said Mr Barroso.

"I was disappointed that there weren't more European leaders who said: of course the Pope has the right to express his views. The problem is not his remarks, but the reactions of the extremists."

Asked why European politicians had been so reluctant to support the Pope, Mr Barroso said "Perhaps because there is concern about a possible confrontation. And sometimes [there is] a sort of political correctness: that one is only being tolerant when placing the opinion of others above one's own. I am very in favour of tolerance, but we should stand up for our values."

Warning about Islamic extremists, the commission chief went on to say that "some of them are very educated people who have studied at our universities. And still, they hate our open societies, our free economies."

"If they are prepared to kill themselves for that, don't you believe they are also prepared to kill us?"

Turkish membership

Asked whether Turkish EU membership could help boost moderate Islam and curb extremism, Mr Barroso said this is a "hypothetical question."

"Turkey is currently not a member and in the short term, accession is not imminent. The EU member states have unanimously decided to open accession negotiations. This takes time, the result is open," he said.

The commission will on 8 November release a report on Turkey's membership preparations, with Mr Barroso saying the document will be "fair and objective" if Turkey has made progress to "possible membership" of the EU – notably he left the possibility of a failure of the talks open.

Centre-right members of the European Parliament last week make a last-minute attempt to insert a paragraph condemning the Muslim outcry over the Pope's speech in the parliament's own report on Turkey, to be voted on in Strasbourg on Wednesday (27 September).

But instead they decided to file an amendment to the report that welcomes the Pope's planned late November visit to Turkey.