Tony Woodhouse, the chair of Unite’s executive council, is said to have deleted the post – on the page of ex-Labour MP Ivan Lewis – as soon as he was alerted to it.
In a screengrab published by the Daily Mail, the comment was left under a Facebook post by Mr Lewis.
The post had explained Mr Lewis’s plans for Bury South, the constituency where he is standing as an independent general election candidate.
The newspaper reported Mr Lewis was “shocked” by the remark and considered it antisemitic.
But Mr Woodhouse was quoted as saying: “‘I have not posted on his website for as long as I can remember.
“I wouldn’t put anything like that in a million years. I don’t even know what it means.”
A Unite spokesperson told Sky News: “Tony Woodhouse’s Facebook account was hacked.
“As soon as he was alerted the post was removed.
“Unite is currently undertaking investigations regarding the hacking of the account.”
Sky News understands Mr Woodhouse contacted Mr Lewis via email after being made aware of the comment.
Senior trade union colleagues of Mr Woodhouse at Unite are said to be taking the matter very seriously.
The term “juju” is commonly used to describe a belief system practiced in West African countries.
Mr Lewis resigned his Labour membership in December last year with an attack on party leader Jeremy Corbyn’s handling of antisemitism allegations.
Mr Lewis told Sky News: “After all the concerns I and others have expressed about antisemitism in Labour I’m speechless at this antisemitic post.
“Mr Woodhouse should either resign or if, as he claims, he has been hacked, identify publicly the person in his circle authorised to post from his account and take appropriate action.”
Mr Lewis had been suspended by Labour since November 2017 amid an investigation into allegations of sexual harassment.
He has denied ever making non-consensual sexual comments or sexual advances towards women.
Among the allegations, it was reported Mr Lewis touched a woman’s leg and invited her to his house at a Labour Party event in 2010, when she was 19.
In his resignation letter to Mr Corbyn, the former Labour minister hit out at a “politically motivated delay” in dealing with his case.
He also told the Labour leader: “All too often you have been unwilling to condemn those whose hatred of Israel becomes Jew hatred.”
Chief Rabbi Ephraim Mirvis, the UK’s most senior Jewish leader, recently branded Mr Corbyn’s claims to be tackling antisemitism within Labour as a “mendacious fiction” and alleged “a new poison – sanctioned from the very top – has taken root” in the party.
In response, Mr Corbyn reiterated that antisemitism “will not be tolerated in any form whatsoever” in Labour.
Unite were Labour’s largest donors in the first two weeks of the general election campaign, including a £3m sum given to the party on 13 November.
Len McCluskey, a close ally of Mr Corbyn, is Unite’s general secretary.