Revelers at the on3 festival in Munich booed and shouted at Doherty, but he carried on singing until organizers removed him from the stage, Bavaria's TZ newspaper reported.
Doherty's tirade was broadcast live on Bavarian public radio, the festival's organizers.
"We decided to stop Peter Doherty's appearance on stage as quickly as possible," organizers Bayerischer Rundfunk said in a statement.
It is the latest in a long line of controversies for the 30-year-old Babyshambles singer, whose career has been marred by drug use and jail time.
The lines come from the first verse of the "Song of Germany" and this verse was used as the national anthem under the Nazis.
While the verse is not banned in Germany, it has not been sung since World War II because of its close links with Adolf Hitler.
Outrage As Pete Doherty Sings Nazi Anthem
Rocker Pete Doherty was hauled off stage at a weekend music festival in Germany after he began signing Nazi anthem “Deutschland, Deutschland ueber alles” during his set.
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