The former mayor of London, chosen last month as Labour’s opponent to Boris Johnson for the 2012 election, campaigned for the Respect-backed councillor hoping to become the east London borough’s first elected mayor.
There were suggestions that by appearing with Lutfur Rahman, suspended from the Labour party in September because of “serious allegations” about his conduct, Mr Livingston could be breaking party rules.
After being deselected, Mr Rahman announced that he was standing as an independent for the vote, which takes place this Thursday. Respect party offered “wholehearted support to Councillor Rahman and his campaign”.
It has previously been alleged that the Spitalfields and Banglatown councillor has connections with the fundamentalist Islamic Forum of Europe (IFE), which operates out of the East London mosque.
Another Tower Hamlets councillor, Helal Abbas, was chosen as Labour’s candidate, prompting the expulsion of eight Labour councillors who refused to support him over Mr Rahman.
Mr Livingstone, who beat Oona King to secure the Labour nomination to run in th 2012 London mayoral election, denied that he had been campaigning for Mr Rahman.
Labour MPs and party members voiced criticism of Mr Livingstone, with the Poplar and Limehouse MP Jim Fitzpatrick calling for an investigation.
But Mr Livingstone said he was only campaigning to beat the Conservative candidate.
He added: "I am disappointed by the way the NEC handled the selection in Tower Hamlets.
“However, my position is clear: I fully support Labour candidates in all elections and I am calling for Tower Hamlets residents to use their first preference vote for our candidate, Helal Abbas.
“A second preference should be used for Lutfur Rahman to keep the Tories out."
Mr Livingstone has been expelled from the Labour party once before – during the 2000 London mayoral race, when he successfully ran as an independent against the Labour candidate, Frank Dobson.