AfD deputy chief Alexander Gauland told a newspaper that Germans would not like to have Boateng, whose father is Ghanaian, as a neighbour.
Boateng, 27, is a defender for German champions Bayern Munich and the national team.
The remark drew immediate condemnation.
Mr Gauland later denied it reflected his own views.
The leader of the AfD, Frauke Petry, apologised for the "impression that has arisen".
The comment was carried by the Sunday newspaper Frankfurter Allgemeine Sonntagszeitung.
Under the headline "Gauland insults Boateng", the article quotes the politician as saying: "People find him good as a footballer, but they don't want to have Boateng as a neighbour."
Germany manager Oliver Bierhoff said people who made such comments "are simply discrediting themselves".
Justice Minister Heiko Maas called them "unacceptable and shabby".
Vice-Chancellor Sigmar Gabriel said the comment showed "that Gauland is not just against foreigners but against the good things about Germany".
'Super footballer'
Mr Gauland said that he had "never insulted Mr Boateng", whom he did not know. He added that he had only "described some people's attitudes'' in a background conversation with the journalists.
AfD leader Frauke Petry told the Bild newspaper that her deputy could not remember making the comment, saying: "Independently of that. I apologise to Mr Boateng for the impression that has arisen."
She later tweeted: "Jerome Boateng is a super footballer who is rightly a member of the German national team. I'm looking forward to the European Championship."
The AfD was started three years ago with a Eurosceptic message and has attracted many voters who are angered by an influx of migrants and by Chancellor Angela Merkel's pro-refugee approach.
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