One of Boris Johnson’s deputy mayors resigned last night in the face of a series of allegations of inappropriate conduct and financial irregularities relating to his former life as a Church of England clergyman.

The announcement came just one day after Ray Lewis, flanked by Mr Johnson, vigorously denied all accusations of impropriety and vowed to remain at City Hall.

Last night, just hours after an independent inquiry into the allegations was launched, Mr Lewis said that he would step down in the face of an “avalanche” of allegations against him. He said that Mr Johnson had “reluctantly accepted” the resignation.

His decision throws Mr Johnson’s administration into complete disarray. The mayor had placed Mr Lewis at the centre of his fight against knife crime at a time when it is the most important issue to be tackled at City Hall.

Mr Johnson had vowed to support him, despite learning that Mr Lewis had been barred from holding office in the Church of England because of an alleged serious misdemeanour.

There were indications last night that Mr Johnson had a hand in the resignation. While the mayor said that Mr Lewis remained an “inspiring figure”, he said his confidence had been shaken by the discovery yesterday that his aide was not a “fully-fledged Justice of the Peace”.

Mr Lewis claimed on Thursday that he was a Justice of the Peace, but this was contradicted yesterday by the Government.

Mr Johnson said: “I still hope that he can clear his name. I cannot deny, however . . . that to be misled on this issue has made it harder for me to give Ray the backing necessary to continue in his role as deputy mayor”.

Mr Lewis said in a statement last night that the “drip, drip” of allegations was getting in the way of important work and he did not want anything to obstruct the Mayor of London’s task. He added that the announcement of an independent inquiry, which was to be headed by Martin Narey, a former director-general of the Prison Service, had done little to calm the avalanche of allegations.

Mr Lewis worked as a clergyman in West Ham, East London, in the late 1990s. The Church of England confirmed that Mr Lewis had faced disciplinary measures between 1999 and 2005 which prevented him from preaching. Mr Lewis was accused of borrowing money from parishioners without paying it back.

Asked on Thursday about allegations concerning sexually-inappropriate behaviour, he said that they were “totally unfounded and complete rubbish”. There were also allegations about the Eastside Young Leaders’ Academy, a youth scheme funded by Mr Lewis in 2003, the mayor’s office confirmed.

A close friend of Mr Lewis told The Times last night: “He resigned because of the pressure on his family, the pressure on the Eastside boys and their parents.”

The resignation is a bitter blow to Mr Johnson, and threatens to derail his youth policy. Mr Johnson had lauded Mr Lewis for his work, saying that his “tough love” policies were directed at deprived youth. Mr Johnson had hoped to spread them across the capital. The mayor has been criticised for not suspending Mr Lewis when he learnt of the allegations.

Mr Lewis thanked Mr Johnson for giving him the opportunity to serve London. He added: “I cannot allow the things that I have been into, up to and around me, to obscure the important business of this mayoral team. For this reason I must step down as deputy mayor with immediate effect.”

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