Brian Paddick, a deputy assistant commissioner and the most senior gay officer in the country, consulted his lawyer after comments by Scotland Yard about evidence that he gave on the shooting to the Independent Police Complaints Commission.

The dispute with Mr Paddick comes as the force carries out a confidential leak inquiry to trace another officer who is suspected of passing on information that Sir Ian had secretly recorded telephone conversations with the commission and Lord Goldsmith, QC, the Attorney-General.

The commission is investigating a complaint from the family of Mr de Menezes, who was shot dead last July in a botched counter-terrorist operation, about what Sir Ian and his staff said about the shooting. The commissioner maintains that he was not told that Mr de Menezes was innocent until mid-morning on the day after the shooting.

Mr Paddick has made a statement to the complaints commission saying that he believes a middle-ranking officer in the commissioner’s private office knew six hours after the shooting that the Brazilian had no connection with terrorism.

On Thursday Scotland Yard .issued a statement saying that the claim was untrue, which led Mr Paddick to seek legal advice on libel. In a twist to the row, it emerged yesterday that Mr Paddick is himself facing a disciplinary inquiry by Scotland Yard watchdogs over an allegation that he revealed confidential information to a journalist. The alleged breached of confidence has no connection with the evidence given to the commission.

A junior officer rang a police whistleblower’s line to say that he overheard a mobile phone conversation by Mr Paddick last month that appeared “improper”. Mr Paddick has been asked to send the Metropolitan Police Authority, which deals with the discipline of top officers, an explanation for the call.

Yesterday Mr Paddick, who is the second in command of beat policing across London, would confirm only that he had seen his lawyer about Scotland Yard comments.

Last year he was one of the senior officers who to head the force’s public response to the July 7 bombings, appearing at press conferences to reassure the public and to comment on developments.

Today, in a letter to The Times, Sir Ian denies that Scotland Yard was in “chaos” in the hours after the shooting. He writes: “This was a very busy, difficult, and fast moving day as we faced what was probably the greatest operational test in the Met’s history.” He adds: “The events of last July provided the Met with nique challenges and unparalleled learning opportunities to which we have already responded.”

But one Metropolitan Police Authority member of the MPA is calling for Sir Ian to go on holiday until the complaintscommission has finished looking at events after the shooting. Damian Hockney said: “Other MPA members have suggested to me that it may be time for Sir Ian to take a period of leave to allow matters to settle.”

He added: “I support this suggestion: irrespective of where the blame lies, this matter has become personalised and Sir Ian is seen to be the issue.”

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