The Tory party and the Church of England were yesterday trading accusations of incompetence following the resignation of Ray Lewis, the controversial deputy appointed by Boris Johnson, mayor of London.

Senior aides to Johnson and David Cameron, the Tory leader, lambasted bishops for “sitting on” a file of damaging accusations made against Lewis when he was a vicar.

A church spokesman accused the Tories of failing to make proper checks on Lewis before appointing him and of ignoring later warnings. The spokesman revealed that the church had alerted Johnson, orally and in writing, about the allegations against Lewis in May.

Chris Newland, chaplain to the Bishop of Chelmsford, said: “Lewis’s ministry was restricted because of very serious allegations. If you want to employ someone in a high-profile job, you check with their employers, you take up their references. None of that was done.”

In a desperate attempt to ensure that Johnson’s first serious crisis does not undermine Cameron’s own position, Nick Boles, a key member of Cameron’s “kitchen cabinet” and one of Johnson’s most senior aides, accused church leaders of negligence. He said they had failed to disclose that they had a dossier of accusations made against Lewis while he was a vicar. “The church sat on it and suddenly decided to bring it into the public [arena] now. Why?” he said.

The church’s dossier contains allegations of sexual misconduct and financial wheeler-dealing involving parishioners. In 1993, three years after he was ordained, Lewis was accused of “sexually inappropriate behaviour” by two members of his congregation at St Matthew’s, West Ham. The women did not contact police but informed the diocesan authorities, leading to Lewis being banned from preaching for six years.

In 1995 he was accused of failing to repay £41,000 that he had borrowed from three parishioners. He was interviewed by police but the investigation was dropped. He was also accused of assaulting pupils linked to an academy he set up in 2002 for black boys.

Lewis has denied the allegations. However, the controversy over his past has led to critics questioning Johnson’s judgment in offering him a high-profile role in his administration.

Yesterday Boles admitted that he had encouraged Johnson to recruit Lewis and said the appointment was made “in a bit of a rush”. He added: “I am willing to take responsibility for encouraging Boris to make this appointment. I don’t defend the appointment. I am happy to take my share of the flak.”

Days after Johnson appointed Lewis, the Bishop of Barking alerted him to the allegations.

“The Bishop of Barking did speak to the mayor at an event at Millwall football stadium on Whit Sunday,” said Newland. Subsequently the Bishop of Chelmsford wrote to Johnson stating that Lewis “did not have permission to exercise his priesthood in the diocese”.

However, the Tories hit back, accusing the church of burying not only the file of complaints against Lewis but also the warning given to Johnson. “It was in about paragraph 10 of a very long letter about a global day of prayer,” Boles said.

“We were relying on the fact that [Lewis] had got Criminal Records Bureau checks and was a charity founder and had been a member of the Church of England. The church did nothing to make the Criminal Records Bureau aware of [the allegations].”

Johnson’s official spokesman went further, criticising the way the church had handled the affair. “If they have a file of allegations of the nature they describe, why did they sit on it for 12 years?” he said.

“They never informed Ray. They never even told him they had decided to discipline him. We are inviting you to consider whether natural justice has [been] applied.”

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