Alexander Gauland, deputy leader of Alternative for Germany, was quoted as telling the Frankfurter Allgemeine Sonntagszeitung newspaper: “People find him good as a footballer. But they don’t want to have a Boateng as their neighbour.”
The newspaper’s front-page headline was “Gauland insults Boateng”.
Berlin-born Bayern Munich defender Boateng has played 57 games for Germany and was a mainstay of the 2014 World Cup-winning team.
He is also in Germany’s squad for the 2016 European Championship, which kicks off June 10 in France.
Justice Minister Heiko Maas called the comment “unacceptable”. He wrote on Twitter: “Anyone who talks like this unmasks himself, and not just as a bad neighbour.”
Anti-immigration talk has helped Alternative for Germany (AfD) to surge in polls over recent months as hundreds of thousands of migrants arrived in the country.
In a statement, Mr Gauland said he “never insulted Mr Boateng”. He said that, in a confidential background conversation, he “described some people’s attitudes” but did not himself comment on Boateng.
AfD leader Frauke Petry told the Bild newspaper that Gauland could not remember whether he had made the comment.
“Independently of that, I apologise to Mr Boateng for the impression that has arisen,” Ms Petry said.