The BBC said the 30-year-old musician drew jeers and was asked to leave the stage at the on3 music festival after he sang, "Deutschland, Deutschland ueber alles ..." which translates into "Germany, Germany above everything," a refrain not typically used since Adolf Hitler's Third Reich fell.
A representative for the singer -- who has been in the news in recent years more for his legal troubles and battle with drug addiction, than for his career achievements -- told the British broadcaster Doherty was "unaware of the controversy" regarding the Nazi connotations of the anthem's rarely used first verse.
"He deeply apologizes if he has caused any offense," the spokesman said.
In a message posted on the music festival's Web site, Doherty's manager Adrian Hunter said the singer "wanted to celebrate his appearance in Munich by assimilating and integrating with the crowd."
"Pete himself is from Jewish descent and has fought against racism and fascism with numerous organizations," the message continued. "This is a subject he feels very strongly about."