When a video of his 2012 comments resurfaced in the Daily Telegraph on Wednesday, Labour Party stood by Mr McDonnell, saying he “takes pride in and stands by his track record of forcefully and justifiably condemning the brutal attacks on the Palestinian men, women and children of Gaza and will always stand up for the victims of such disproportionate violence.”
Mr McDonnell tweeted that the newspaper was "doing a number" on him.
The Board of Deputies demanded he apologise to the Jewish community for his “wild claims”.
The Daily Telegraph also reported that Mr McDonnell shared a platform with suspended Labour activist Jackie Walker – despite party colleagues warning against doing so.
Ms Walker was suspended twice by the party in 2016 over comments in which she referred to Jews as the “chief financiers of the slave trade”, and for remarks she made about Holocaust Memorial Day.
Karen Pollock, the chief executive of the Holocaust Educational Trust, tweeted on Thursday: “Just a few days ago John McDonnell said that allegations of antisemitism in the Labour Party had shaken him to the core, yet just a few months after Jackie Walker claimed Jews were chief financiers of the slave trade - a hugely offensive remark.
“It seems he insisted on sharing a platform with her, despite calls for him not to. Meanwhile, his use of the term genocide is not only inaccurate, but irresponsible and deeply offensive, as Mr McDonnell should know.”
In response, the Labour Party said Ms Walker had not been suspended when the two shared a platform.