Ephraim Mirvis delivered the warning ahead of Britons going to the poll on December 12 that “the overwhelming majority of British Jews are gripped by anxiety”.
The shock intervention likely to derail the launch of Labour’s race and faith manifesto, which is to be released tomorrow.
Labour has been riddled with complaints about anti-Semitism but Jeremy Corbyn has previously underlined it is tackling the issue by expelling members.
A Labour Party spokesman said: “Jeremy Corbyn is a lifelong campaigner against anti-Semitism and has made absolutely clear it has no place in our party and society and that no one who engages in it does so in his name.
“A Labour Government will guarantee the security of the Jewish community, defend and support the Jewish way of life, and combat rising anti-Semitism in our country and across Europe.”
But Mr Mirvis said he feared the future for Jews in Britain if Labour came to power.
He said: “During the past few years, on my travels through the UK and further afield, one concern has been expressed to me more than any other. Of course, the threats of the far right and violent jihadism never go away, but the question I am now most frequently asked is: What will become of Jews and Judaism in Britain if the Labour Party forms the next Government?”
He said that the “Jewish community has watched with incredulity as supporters of the Labour leadership have hounded parliamentarians, members and even staff out of the party for challenging anti-Jewish racism”.
He added: “The way in which the leadership has dealt with anti-Jewish racism is incompatible with the British values of which we are so proud – of dignity and respect for all people. It has left many decent Labour members both Jewish and non-Jewish, ashamed of what has transpired.”
He concluded: “It is not my place to tell any person how they should vote. I regret being in this situation at all. I simply pose the question: What will the result of this election say about the moral compass of our country? When December 12 arrives, I ask every person to vote with their conscience. Be in no doubt, the very soul of our nation is at stake.”
Additional reporting by Liz Perkins.