According to the Standard, Mr McDonnell linked to the Innovative Minds website in a post promoting the boycott of Israeli goods. The website linked to articles that were sympathetic about at least two suicide bombers – including one, who murdered 19 Israelis outside a nightclub.
Another article on the website, posted in 2002, said the state of Israel should be “dismantled”.
A spokesman for Mr McDonnell said the link to the website would be removed immediately, the paper reported.
He added: “John was supporting a peaceful campaign against the bombing in Gaza at the time in 2014. The campaign suggested using the link to this website in order to take part.
"He was obviously not aware of the views this website historically expressed 10 years previously but John’s office has subsequently removed the link in question immediately.
"John has a zero tolerance approach to antisemitism and has a record of campaigning against all forms of racism.”
Sir Eric Pickles, chairman of Conservative Friends of Israel and the UK’s Special Envoy for post-Holocaust issues, said that Mr McDonnell’s call against antisemitism lacked “credibility”.
He said: “As well as promoting the boycotting of Israeli goods, these extremely unpleasant and antisemitic websites host extremist content, including tributes to suicide bombers and calls to jihad- the stated purpose of which is to ‘spill the blood’.
“The Shadow Chancellor has called for antisemites to be expelled from the Labour Party, he is right to do so, for their presence threatens the very soul of a once great party. But that call lacks credibility, when he himself endorses antisemitic boycott groups The only way Labour, and its leadership, can rid itself of antisemitism is to cease keeping company with antisemites.”
The Labour party has been contacted for comment.
The allegation comes after a Daily Mail report accused Mr McDonnell of publishing controversial articles during his tenure as co-editor of the left-wing Herald newspaper.
As well as calling for the abolishment of private property, the report claimed that Mr McDonnell oversaw the publication of allegedly antisemitic articles.
In 1985, one Herald article reportedly compared the Israeli government to the Nazis after claiming authorities confined Palestinians to ‘concentration camps’.
A few weeks later, the paper endorsed terror attacks against Israeli authorities, to counter what it described as ‘the racism at the heart of the Israeli state’.
