Pink Floyd s Roger Waters is a well-known pro-Palestinian activist (Photo: AFP)
Waters sparked an uproar after images on social media showed him wearing a long, black coat with red armbands on stage at the Mercedes-Benz arena last week.
Berlin police said they were probing Waters for incitement to hatred and Germany's official in charge of fighting anti-Semitism called for Waters to be held accountable.
Wearing or display of symbols evoking the Nazi era are crimes in Germany.
In a statement released on Saturday Waters dismissed the criticism as politically motivated.
"My recent performance in Berlin has attracted bad faith attacks from those who want to smear and silence me because they disagree with my political views and moral principles," he said in the statement that was posted on his Twitter account.
Waters is a well-known pro-Palestinian activist who has been accused of holding anti-Israeli views. He has floated an inflatable pig emblazoned with the Star of David at his concerts.
Waters has played in several German cities in recent weeks as part of his "This Is Not A Drill" tour.
But it has been hugely controversial with some city officials even trying, unsuccessfully, to ban him from performing.
The "Another Brick In The Wall" singer denies the anti-Semitism accusations, saying he protests against Israeli policies and not the Jewish people.
"The elements of my performance that have been questioned are quite clearly a statement in opposition to fascism, injustice and bigotry in all its forms," Waters said in his statement.
"The depiction of an unhinged fascist demagogue has been a feature of my shows since Pink Floyd's 'The Wall' in 1980," he said.
At the same Berlin concert, Waters also flashed the names of several deceased people on a large screen, including that of Anne Frank, the Jewish teenager who died in a Nazi concentration camp.
Also named was slain Palestinian-American journalist Shireen Abu Akleh, killed by Israeli forces, prompting criticism that Waters was relativising the Holocaust.
Waters is due to play his final German concert in the western city of Frankfurt on Sunday evening, and protesters are planning to demonstrate outside the venue.
Frankfurt city authorities sought to stop the concert but a court ruled against them, citing artistic freedom.
* This story has been edited by Ahram Online.