The musician, 79, wore a black trench coat with a pink armband as he appeared to imitate the SS outfit from World Struggle Two.
He pretended to shoot on the crowd with a faux gun whereas an inflatable pig bearing the Star of David floated above.
The names of Holocaust victims, together with diarist Anne Frank, have been projected on a display on the present final week.
The Jewish Information mentioned Berlin police have launched a felony investigation “concerning the suspicion of incitement of the individuals”.
Police chief Martin Halweg advised the paper his costume could possibly be seen as glorifying the violent rule of the Nazi regime.
Labour MP Christian Wakeford is amongst those that have condemned the musician over his “divisive actions”.
Mr Wakeford, who represents Bury South, mentioned Mr Waters shouldn’t carry out in Manchester amid fears he may gas anti-Jewish hatred.
Mr Wakeford advised MPs he was “involved” about Mr Waters enjoying on the AO Enviornment on June 10.
“The town of Manchester has a wealthy and vibrant historical past by which these of various faiths and backgrounds have lived collectively in addition to stood collectively by means of troublesome occasions and occasions of division,” he mentioned.
Israel’s Overseas Ministry criticised Mr Waters on Twitter, writing: “Good morning to each one however Roger Waters who spent the night in Berlin (Sure Berlin) desecrating the reminiscence of Anne Frank and the six million Jews murdered within the Holocaust.”
It added: “Nice information! Berlin police have launched a felony investigation.”
US marketing campaign group StopAntisemitism additionally accused Waters of “denigrating” the homicide of Frank.
Earlier this yr, Mr Waters was accused of being “antisemitic to your rotten core” by Polly Samson, spouse of his ex-Floyd bandmate David Gilmour.
The bassist says he’s talking out in opposition to Israel’s therapy of Palestinians. He started his Berlin present by insisting he isn’t anti-Semitic.