Shortly after the complaint, the Guardian said it had "taken down the letter pending investigation".
Mr Williamson, whom the Board of Deputies has accused of "Jew-baiting", was supended in February for saying that the Labour party had been "too apologetic" about antisemitism.
His readmission last month triggered a public outcry and he was resuspended two days later.
On Tuesday, Labour referred his case to a fresh disputes panel.
One signatory to the Guardian letter was listed as representing anti-racist campaigners Hope Not Hate. But the group said they had “no knowledge” of them and would ask the paper to remove their name.
The Board's complaint said: "One signatory – Meredith Wood-Bevan – claims to represent the anti-racist organisation Hope Not Hate.
"Hope Not Hate themselves have complained that they have no knowledge of this person, and certainly did not authorise her to sign on their behalf.
"Another signatory – Peter Sheridan – claims to represent the Jewish Labour Movement, despite the Jewish Labour Movement being categorical in its opposition to Chris Williamson’s readmission to the Labour Party.
The complaint said the paper had been inaccurate when it referred to the signatories as "prominent members of the Jewish community" because many names "are completely unknown and unverified".
It added: "The Guardian has a duty to conduct due-diligence on the signatories of letters it publishes, especially on one relating to such a serious issue as racism.
"In this case, the inclusion of racist signatories ought to have stopped the publication of the letter."
Also among the signatories is Michael Morgan, who lists himself as a member of the Scunthorpe Labour party. Mr Morgan was suspended from the party in 2016 after his tweets came to light.
These included saying “thankfully the Hispanics are outbreeding the Jews in New York”, “I have many friends who are true Jews, not Ashkenazi bastardised, pseudo-Judaic, quasi semites” and talking about the “ongoing perversions of the Talmud Jews.”
Also listed is Elleane Green, the creator of the “Palestine Live” Facebook group, where antisemitism and Holocaust denial were regularly shared.
Ms Green shared material from antisemitic and Holocaust denial outlets including Veterans Today and The Ugly Truth, and liked posts describing how “the Jewish minority have far too much say in this country.”
The letter was shared by the fringe Jewish Voice for Labour group, which has repeatedly denied the extent of antisemitism within Labour.
Last week, JVL published a link to the “Jewish petition in support of Chris Williamson”, urging members to sign it.
Signatory Professor Noam Chomsky has publicly defended Robert Faurisson, a Holocaust denier with links to neo-Nazi groups, saying that he had found “no evidence” that Faurisson was either of those things and calling him “a relatively apolitical liberal”.
Richard Falk gave a cover endorsement for The Wandering Who, a book by notorious antisemite Gilad Atzmon, which, describes Jews as “the only people who managed to maintain and sustain a racially orientated, expansionist and genocidal national identity that is not at all different from Nazi ethnic ideology”.
Tony Greenstein and Jackie Walker, who were both expelled by Labour over their comments about antisemitism, also signed the letter.
Ms Walker was suspended after saying “many Jews were chief financiers of the slave trade”.
She was readmitted but then re-suspended and later expelled after telling people that she hadn’t found a definition of antisemitism that she “could work with”.
Mr Greenstein was suspended and later expelled after verbal abuse of the Jewish Labour MP Louise Ellman, whom he called a “racist supporter of the child abuse of Palestinian children”.
Mr Greenstein, who is Jewish, described another Jewish woman as “a poisonous little brew supports Zio Labour Movement – she’s the British version of Irma Grese, Nazi b***h hanged at Belsen.”
The Guardian has been approached for comment.
