Laurence Lustgarten, a barrister and commissioner of the Independent Police Complaints Commission (IPCC), was put on gardening leave last month after the allegation by a female colleague.

The decision was revealed this weekend by senior Scotland Yard sources unhappy with the way the IPCC has conducted an inquiry that could lead to the resignation of Sir Ian Blair, the Metropolitan police commissioner.

The disclosure signals an escalation in hostilities with the regulator over its probe into the shooting of Jean Charles de Menezes at Stockwell Tube station, south London, last July during the hunt for terrorist suspects.

In a separate development, the IPCC faces further disruption at senior levels with the resignation of its chief executive, Susan Atkins. The commission said she had decided to leave because of a management reorganisation.

Lustgarten is a leading liberal lawyer, an expert on human rights and one of four IPCC commissioners responsible for overseeing complaints against the Met. A visiting professor of law at King’s College London, he is one of 15 commissioners on the IPCC board.

He is not directly involved in the investigation into the Stockwell shooting. But some Scotland Yard officers are seizing on the disclosure that the IPCC is now investigating one of its own commissioners, to question its authority to judge the conduct of others.

The briefing war between the two bodies is intensifying as the IPCC moves closer to completing its inquiry into whether Blair and other senior Met officers told the truth about the shooting. Last week Lustgarten would only say: “There have been a number of difficulties but it’s a bit difficult to discuss them at the moment.”

Friends say he is baffled by the allegations, which he vigorously denies. “Laurence hasn’t seen this woman for over a year,” said one. “He hasn’t had the full facts about what he’s supposed to have done to her other than that it’s supposed to be sexually inappropriate.” An IPCC spokeswoman declined to comment on Lustgarten.

The commission says Atkins’s departure is unconnected with the De Menezes inquiry. A spokeswoman for the commission denied newspaper reports that Atkins’s resignation was prompted by leaks of the investigation’s progress. She said the chief executive’s job had been combined with another post which Atkins did not wish to take on.

Atkins, a former Home Office civil servant, ran the IPCC’s administration and, said the spokeswoman, was “not involved in any IPCC investigations”.

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