Starmer decided not to restore the Labour whip to Corbyn on Wednesday, even though his predecessor’s party membership has been reinstated by the Labour’s ruling body.
The watchdog found the party committed unlawful acts of harassment and discrimination while Corbyn was leader.
In response Corbyn said allegations about anti-Semitism had been “dramatically overstated” by his political opponents.
McCluskey led calls from the Labour left for Starmer to “pull back from the brink” and urged him “in the strongest possible terms” to reconsider his decision.
The union leader tweeted that he was “astonished”, and added: “This is a vindictive and vengeful action which despoils party democracy and due process alike and amounts to overruling the unanimous decision of the NEC panel yesterday to readmit him to the party.”
After clarifying his remarks on Tuesday, Corbyn was reinstated as a member, but Starmer said Corbyn’s original remarks “undermined” the party’s work rebuilding trust with Jewish communities.
McCluskey added he believed the move by Starmer, who took over from Corbyn in April showed “marked bad faith”.
He said: “The continued persecution of Jeremy Corbyn, a politician who inspired millions, by a leadership capitulating to external pressure on Party procedures risks destroying the unity and integrity of the Party. I urge Keir Starmer in the strongest terms to pull back from the brink.”
The Socialist Campaign Group of Labour MPs, which includes former shadow chancellor John McDonnell and former shadow home secretary Diane Abbott, also issued a joint statement opposing the decision.
Signed by 32 MPs, it said it was “correct” of the National Executive Committee to reinstate Corbyn’s membership, adding: “In light of this, the decision to not restore the whip to Jeremy Corbyn is wrong and damaging to the Labour Party.
“This decision and the division it causes severely undermines efforts to unite to defeat antisemitism and fully implement the EHRC recommendations and to challenge and defeat this disastrous Conservative government.
“It should be swiftly reversed.”
Momentum, the campaign group launched to support Corbyn’s leadership, called the decision a “joke” and has started a petition.
The petition read: “In his leadership campaign, Starmer promised party unity and progressive policy. So far he’s launched a vindictive campaign against everyone from Corbyn to CLP members, and done a U-turn on the public ownership of the big energy companies.
“Rather than fighting a corrupt Tory party, he’s trying to destroy the left.”
The petition has so far received just over 1,000 signatures.
Starmer’s decision has, however, been welcomed by Jewish groups and prominent Jewish Labour MP Margaret Hodge, who was reportedly prepared to resign from the party.
A snap YouGov poll found that 50% of the public thought Starmer was right not to allow Corbyn’s return to the Labour benches, while 21% thought he was wrong.
Starmer said: “Jeremy Corbyn’s actions in response to the EHRC (Equality and Human Rights) report undermined and set back our work in restoring trust and confidence in the Labour Party’s ability to tackle anti-Semitism.
“In those circumstances, I have taken the decision not to restore the whip to Jeremy Corbyn. I will keep this situation under review.
“Since I was elected Labour leader, I have made it my mission to root out antisemitism from the Labour Party.
“I know that I will judged on my actions, not my words.
“The disciplinary process does not have the confidence of the Jewish community. That became clear once again yesterday.
“It is the task of my leadership to fix what I have inherited. That is what I am resolute in doing and I have asked for an independent process to be established as soon as possible.
“I’m the leader of the Labour Party, but I’m also the leader of the Parliamentary Labour Party.”