Mr Seehofer’s controversial remarks echoed last year’s election slogans from the nationalist Alternative for Germany party (AfD), which campaigned on an anti-Muslim platform.
But they were most clearly aimed as a broadside against Mrs Merkel, who famously declared “Islam belongs in Germany” in a 2015 press conference after opening the country’s borders to over 1 million asylum-seekers.
“Islam does not belong in Germany,” Mr Seehofer told Bild newspaper. “Germany is shaped by Christianity. That means not working on Sundays and celebrating religious holidays such as Easter, Pentecost and Christmas.
“Of course the Muslims who live with us belong in Germany. But that doesn’t mean we should give up our national traditions and customs.”
The leader of Mrs Merkel’s Bavarian sister party, the Christian Social Union (CSU), Mr Seehofer was the leading opponent of her refugee policy and the dispute almost ended the longstanding alliance between the two parties.
But they patched up their differences ahead of last year’s election and Mr Seehofer was given control of migration and asylum policy as interior minister under the new coalition deal. His remarks on Friday suggest he is ready to reopen the feud in government.
Mrs Merkel responded angrily to Mr Seehofer’s comments. “We want an Islam based on the constitution and compliant with constitutional law,” she said on a visit to Paris. “I think we must do everything we can to allow religions to live together in peace.”
Mr Seehofer also came under attack from Annegret Kramp-Karrenbauer, the chairman of Mrs Merkel’s Christian Democrat party (CDU) who is widely seen as her chosen successor.
“Freedom of religion undoubtedly belongs in Germany, just as the Muslims in Germany, together with their faith, belong in our country,” Ms Kramp-Karrenbauer said.
More than 4 million Muslims live in Germany, 1.9 million of whom are German citizens. More than 60 per cent are of Turkish heritage and were living in Germany long before Mrs Merkel’s decision to open the borders to asylum-seekers.
Mr Seehofer later sought to clarify his remarks. “Our country Germany has been shaped by Christianity for centuries. That’s why it’s wrong to say Islam belongs in Germany, ” he said.
“Of course we have tolerance and respect for other religious communities. And of course the Muslims living in Germany belong in Germany.”
It was Wolfgang Schäuble, the former finance minister and current speaker of the German parliament, who first declared in 2006 that “Islam is part of Germany and Europe”.
The phrase at the centre of the dispute,“Islam belongs in Germany” was first coined in 2010 by Christian Wulff, the Germna president at the time, and later taken up by Mrs Merkel.
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Read more: From 2017/12/30