Interior Minister Hans-Peter Friedrich said the study's results were worrying, according to in an interview published on Thursday.
“Germany respects the background and cultural identity of its immigrants. But we don't accept the importation of authoritarian, anti-democratic and religiously fanatical points of view,” Friedrich told the Bild newspaper.
Whoever fights against freedom and democracy will not have a future here, said the minister - a member of the ruling Christian Democratic Union's sister party, the Christian Social Union.
The survey showed that of Muslims living in Germany who were not German citizens, 52 percent favored integration, while 48 percent “strongly leaned toward separation” and clearly rejected German majority culture.
But when taking into account both Muslims who were German citizens and those who were not, the figure rose to 78 percent in favor of integration, versus 22 percent who favoured a more separatist approach.
The interior ministry's study, “The Daily Life of Young Muslims in Germany” surveyed Muslims between 14 and 32 who had not become German citizens. It also interviewed several generations of Muslims living in Germany and evaluated television programmes.
There are currently around four million Muslims living in Germany, of which nearly half are German citizens.
The survey also showed that among the 14 to 32-year-olds there exists a "subgroup" of religious extremists who hold anti-western views and are reportedly prepared to use violence.
This group amounts to about 15 percent of Muslims with German citizenship and about 24 percent for Muslims who are not German.
Hans-Peter Uhl, the domestic affairs spokesman of the CDU/CSU faction in the German parliament, the Bundestag, told the Neue Osnabrücker Zeitung that the high number of Muslims who don't want to integrate is “alarming.”
“Rejecting integration can, but it doesn't have to, provide fertile ground for religious fanaticism and terrorism,” Uhl said in an article published Thursday. Uhl is calling for non-German Muslims to show proof of their integration.
The study was criticized by the Free Democratic Party, the government's junior coalition partner.
"I have to wonder that the BMI (Interior Ministry) used taxpayers' money to finance a study that produces headlines but no findings," said Serkan Tören, the FDP's parliamentary faction speaker for domestic politics.
Tören said religious commitment among young Muslims is often an "empty shell" that has nothing to do with actual religious practice but with "provocation and cultural segregation."
The German-Turkish politician said there is no automatic connection between religion and violence. "Other studies and my personal experience show that."
Wolfgang Frindte, a psychologist and a key investigator for the study, said its results did not surprise him.
He told news magazine Spiegel Online that the number of Muslims living in Germany who hold radical views is decreasing, as more Muslims distance themselves significantly from Islamic terrorism.