Bavaria’s finance minister, Markus Söder, said the German people “do not want a multicultural society” and recommended they should be sent back over the next three years.
More than one million refugees have arrived in Germany over the past year, sparking backlash among critics of Chancellor Angela Merkel’s open-door policy.
Many migrants have been re-settled in the minister’s state in the south of the country.
Mr Söder said integration of those from different cultural backgrounds was “bound to fail”.
He added: “Even with the best intentions in the world, it will not work to integrate successfully that many people with a completely different cultural background.
“Germans do not want a multicultural society.
“Anyone who wants to live here must adjust themselves to our values and not vice-versa.”
The CSU minister added the asylum seekers pose a security threat because of few details about their background.
He also said many parts of war-torn countries such as Iraq and Afghanistan have been recognised as safe.
The 49-year-old added: “The civil war in Syria will also end sometime soon.
“According to legislation, people have to return home when the reason for fleeing is no longer valid.”
Bavarian prime minister Horst Seehofer has also blasted Angela Merkel’s government
This is not the first time Mr Söder has hit out at the German chancellor’s policies.
He blasted Angela Merkel earlier this year for allowing so many refugees to enter Germany, saying: “It is a big mistake to open the borders without any checks.”
And other Bavarian politicians have slammed Merkel – who fewer than half of Germans now support.
In July, prime minister Horst Seehofer accused her of “hypocrisy” and failing to face up to her government’s responsibilities.