The veteran left-wing ally of Jeremy Corbyn also asked everyone at the meeting - which voted to adopt to party's new code on Jew-hate instead of the internationally recognised definition - to raise their hand if they had witnessed anti-Jewish conduct.
But in a letter General Secretary Jennie Formby sent to the JLM on Thursday, she says that, following Mr Willsman's decision to apologise, she has "written to him reminding him about the high standard of conduct we expect from all members - particularly those serving on the party's governing body.
"I have made clear any repetition of similar conduct is likely to result in formal disciplinary action."
Ms Formby's letter said that the party's Governance and Legal Unit had "sought to ascertain what was said with a view to determining whether to open a formal investigation of his conduct".
Sources told the JC that the decision not to launch a formal investigation into Mr Willsman's remarks has "infuriated" JLM's own ruling committee.
A source added: "It's one of the most blatant cases of the Labour leadership looking after their left-wing mates.
"Willsman's remarks at the NEC meeting were inflammatory to say the least. And it's not the first time he's strayed into dubious territory when it comes to discussing Jews."
The source compared Mr Willsman's treatment with Labour MP Dame Margaret Hodge, who received a formal warning about disciplinary proceedings within 12 hours of calling Mr Corbyn "antisemitic and a racist" to his face.
"This just looks like Pete Willsman has been tipped off about complaints against him and has been told to issue an apology himself to stop the need for an investigation," the source added. "The whole thing stinks."
Mr Willsman, who is now standing for election to remain a candidate on the NEC, said in his apology: “At the NEC... I spoke in support of the decision to confirm the adoption of the Code of Conduct on antisemitism and to reopen development of the code in consultation with Jewish community organisations.
"Not all of what I said has been accurately reported.
"But I accept that what I did say, and the way I said it, fell short of the requirement, which I accept, for discussions of contentious issues to be conducted in a fully civil and respectful way.
"I deeply apologise for any offence caused to those present and those to whom my remarks were reported."
In a letter of complaint to Labour, the JLM said they believed Mr Willsman's comments fell foul of the code of conduct by clearly “stereotyping” and using “insensitive and incendiary language, metaphors, distortions and comparisons”.
They added he had breached point nine, which describes “stereotypical and negative physical depictions/descriptions or character traits, such as references to wealth or avarice and -- in the political arena -- equating Jews with capitalists or the ruling class”.
JLM's letter of complaint to Ms Formby added: "In 2016, in her Report, Shami Chakrabarti wrote 'any seasoned activist who says that they are completely unaware of any such discourse must be wholly insensitive or completely in denial'. Mr Willsman has brought the Party into disrepute by denying the existence of antisemitism."
Mr Willsman is standing for re-election onto the NEC as part of a slate of candidates backed by left-wing group Momentum.
