GMB chief Tim Roache has sought to calm a bitter row over a leaked Labour report on the party's handling of anti-Semitism allegations.
GMB members at Labour HQ voted for a motion accusing the party's general secretary Jennie Formby of leaking the report to the media.
They said they no longer had confidence that their welfare was her priority.
Mr Roache insisted the GMB was "not going for" Ms Formby after a social media backlash.
The document at the centre of the row was published internally in March and leaked to the media this month.
The 860-page dossier was put together in response to the Equalities and Human Rights Commission investigation into Labour's handling of anti-Semitism cases.
It acknowledged the scale of the party's problem with anti-Semitism and detailed efforts to reform disciplinary procedures led by Ms Formby, who became general secretary in 2018.
But it also alleged these efforts were hampered by factions hostile to the party's former leader, Jeremy Corbyn, and said some in Labour headquarters were working against a party victory at the 2017 general election.
The names of current and former staff members had not been redacted in the copy of the report leaked to the media.
And the document also included alleged records of private discussions between party staffers, in which they use derogatory language about Labour members and Mr Corbyn, and criticised the party's policies.
On Thursday, GMB members at Labour Party HQ voted to back a motion calling on Ms Formby - a key ally of Mr Corbyn - to "personally apologise to the current staffers named in the report".
It accused Ms Formby of "trawling the emails and instant messenger logs", and claimed the general secretary had "effectively unilaterally placed all members of staff under investigation" without due process.
The motion also referred to a "hostile environment created post-2015" when Jeremy Corbyn was first elected leader, "in which staff who did not appear to support the new leader were marginalised, ignored, harassed and hounded out of the party".
And it added: "Staff can no longer be confident that the general secretary has the safety and welfare of staff as her top priority, and [she] has allowed the mental and physical wellbeing of staff to be put at risk with the creation and leaking of this report."
But, writing on Twitter, Mr Roache said this was not a vote of no confidence, adding: "The GMB is NOT going for Jennie. FACT."
In a statement, the union leader said: "Any racism or discrimination - on any side - based on race, gender, disability or political belief is utterly unacceptable.
"Leaking an un-redacted report, containing names and personal messages of employees and the names of people who made complaints about racism on the understanding of anonymity, is unacceptable.
"Both things can be wrong without condoning the other."
The report has prompted an angry backlash among supporters of the former leader, who was succeeded by Sir Keir Starmer at the start of April.
Some have threatened on social media to leave the party, while others have vowed to stay and fight for the left-wing policies championed by Mr Corbyn.
Sir Keir has ordered an investigation into the contents of the report and how it was leaked, saying it raised "a number of matters of serious concern".
Speaking about the investigation, he told the BBC on Friday: "I want it to be speedy. It's more likely to be a few weeks or months - no longer than that. We haven't got a timeline on it at the moment but it must be swift."
He said he wanted to "let that investigation run its course and look at the findings when they're available to me before jumping to conclusions" about whether Ms Formby could stay in her post.
Mr Roache said he backed an independent inquiry "in which all sides can have faith is a responsible, reasonable and welcome step to determine exactly what happened in all aspects of this situation".
He added: "It is only with all of the facts to hand - not one version handed to the media in order to advance one political agenda or another - that a proper judgment can be made."