The Unite general secretary said he was sorry “if” his language caused hurt after deploying what critics said was an anti-Semitic trope.
Asked about Lord Mandelson’s opinion on Keir Starmer, Mr McCluskey told BBC Newsnight: “I stopped listening to what Peter Mandelson said many many years ago.
“I would suggest that Peter just goes into a room and counts his gold, not worry about what’s happening in the Labour Party.
“Leave that to those of us that are interested in ordinary working people.”
The comments sparked an angry backlash on Twitter.
Labour peer Andrew Adonis tweeted: “If Len McCluskey doesn’t realise that ‘count his gold’ is one of the oldest antisemitic tropes in the whole of history, he was born yesterday.”
Rebecca Filer, national organiser for Jewish Labour, added: “Awful to see Len McCluskey using an antisemitic trope to refer to Peter Mandelson going to ‘count his gold’ on Newsnight tonight.”
Mr McCluskey, an ally of Jeremy Corbyn, later tweeted: “Before this gets out of hand, let me say language is important and I apologise to Peter Mandelson and anyone else if mine has caused hurt.”
BBC Newsnight said he maintained his use of language was not anti-Semitic.
Examples of possible anti-Semitism listed by the International Holocaust Remembrance Alliance include “mendacious, dehumanizing, demonizing, or stereotypical allegations about Jews as such or the power of Jews as collective”.
The comments came as part of a Newsnight documentary which interviewed key figures on both wings of the Labour Party about its future and Jeremy Corbyn’s legacy.
Lord Mandelson, who resigned twice from Tony Blair’s government including after questions about his involvement with an Indian tycoon’s passport application, branded Jeremy Corbyn’s leadership “toxic, sectarian and backward-looking” on the special.
But left-winger Diane Abbott said she was “suspicious” of new leader Keir Starmer when he was in the shadow Cabinet.
She added: “Keir Starmer’s ambition is fairly apparent. And I think it’s noticeable, having been Mr Remain all the way up until he got leadership of the party, you don’t hear much from Keir about Remain now.
“I think it’s fairly apparent that Keir had other motives.”
Lord Mandelson’s grandfather was Jewish and founded the Harrow United Synagogue.
In a 2010 interview he said his father was atheist but became “overtly Jewish” during the 1967 Six Day War and the 1973 Yom Kippur War.
“My father became very militant and really emotional when Israel was under attack. In a sense it was the same for me,” he told the JC. He added: “It’s not that I am religious. It’s the extended family, which part of me wants to be part of.”