Cries of "the Jews killed Jesus" rang from the Kedem picket when Vivian Wineman visited on Wednesday.
The president of the Board of Deputies had come to Manchester to view for himself the ongoing protests outside the Israeli-owned cosmetic store and the barracking from the pro-Palestinian activists.
He said: "This has been an unfolding situation. It's not until you actually see it, that it's clear this protest is not about Israel but about Jews.
"And while only some of the boycotters have been antisemitic, it offers very little comfort to Jewish people."
Greater Manchester Police said nine protesters had been arrested over the weekend.
It's clear this protest is not about Israel but about Jews
Police are investigating a protester who posted selfies on Facebook in Saudi Arabia, picturing himself holding an automatic rifle and declaring that he wanted to "wipe out the Jews who are attacking Palestine". The man, from north Manchester, attended a protest a week ago.
Lawyers acting for Kedem have called on Manchester's chief constable to use legal powers to move the picket permantly away from the shop. Police said they were reviewing whether to use the powers before the weekend when more protests are expected.
Meanwhile Mr Wineman has agreed to meet the woman behind a campaign calling on the Board to take a firmer stand against antisemitism. Victoria Slotover's online petition has attracted over 500 signatures.