AfD vice president Alexander Gauland told a daily paper that Germans might not want to have Boateng, whose father is Ghanaian, as a neighbor.
Boateng, 27, is a safeguard for German champions Bayern Munich and the national group.
The comment drew quick judgment.
Mr Gauland later denied it mirrored his own perspectives.
The pioneer of the AfD, Frauke Petry, apologized for the "feeling that has emerged".
The remark was conveyed by the Sunday daily paper Frankfurter Allgemeine Sonntagszeitung.
Under the feature "Gauland affronts Boateng", the article cites the government official as saying: "Individuals discover him great as a footballer, however they would prefer not to have Boateng as a neighbor."
Germany chief Oliver Bierhoff said individuals who made such remarks "are essentially defaming themselves".
Equity Minister Heiko Maas called them "unsatisfactory and shabby".
Bad habit Chancellor Sigmar Gabriel said the remark demonstrated "that Gauland is against outsiders as well as against the great things about Germany".
'Super footballer'
Mr Gauland said that he had "never offended Mr Boateng", whom he didn't have even an inkling. He included that he had just "portrayed some individuals' states of mind'' in a foundation discussion with the writers.
AfD pioneer Frauke Petry told the Bild daily paper that her appointee couldn't made the remark, saying: "Freely of that. I apologize to Mr Boateng for the feeling that has emerged."
She later tweeted: "Jerome Boateng is a super footballer who is appropriately an individual from the German national group. I'm anticipating the European Championship."
The AfD was begun three years prior with an Eurosceptic message and has pulled in numerous voters who are rankled by a deluge of transients and by Chancellor Angela Merkel's master evacuee approach.
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