Scotland Yard has announced it has moved a top officer who had risen to become head of counter-terrorism after he was caught up in the Stephen Lawrence spying scandal.

Commander Richard Walton has been moved "temporarily" from his post as head of the Metropolitan police's counter-terrorism command and has been referred by his force to the Independent Police Complaints Commission (IPCC).

The move came after a report by Mark Ellison QC commissioned by the home secretary found that during the 1998 Macpherson inquiry into the Lawrence case the Met had a spy in the Lawrence camp.

Codenamed N81, the spy secretly passed "fascinating and valuable" intelligence on to a senior Met officer, Richard Walton, who was involved in drafting the then Met commissioner Sir Paul Condon's defence of his force's conduct during the investigation.

Walton was moved on Friday to a non-operational role. It comes as the Met faces withering criticism from the home secretary downwards over the new revelations about its behaviour during the Lawrence case.

In a statement the Met said: "Following the publication of the Ellison report, the deputy commissioner of the Metropolitan police, Craig Mackey, has today made the decision to move Commander Richard Walton temporarily from his post as head of the counter-terrorism command, SO15, to a non-operational role. The Metropolitan police has voluntarily referred the matter to the IPCC."

The head of the Independent Police Complaints Commission (IPCC), Dame Anne Owers, said she had apologised to the Lawrence family for the police watchdog's part in prolonging the "family's search for the truth". Owers said the Ellison review made it clear that a 2006 IPCC investigation was "wrong" to conclude there was no evidence to suggest Scotland Yard withheld information in relation to corruption from the Macpherson inquiry into Stephen Lawrence's death.

She said: "I fully recognise this has prolonged by many years the Lawrence family's search for the truth about the failed investigation into their son's murder. I have today written to Baroness Lawrence and Mr Lawrence to apologise for our part in this."

Earlier Sir Bernard Hogan-Howe said the publication of the "devastating" Ellison report, which found the Metropolitan police spied on the Lawrence family, marked one of the worst days in his police career.

The Metropolitan police commissioner vowed on Friday to reform the force, which is the largest in Britain and whose leaders have made similar pledges in the past.

It was the first time Hogan-Howe had commented since publication on Thursday of the report from Ellison into allegations of corruption shielding the killers of Lawrence and into undercover officers spying on the dead teenager's grieving family.

Hogan-Howe said: "This was a devastating report for the Metropolitan police and one of the worst days that I have seen as a police officer."

Ellison's finding that the Metropolitan police planted "a spy in the Lawrence family camp" led the home secretary to order a judge-led inquiry into undercover policing.

After leaving his deputy to give the force's reaction to the report on Thursday, Britain's most senior officer said: "To see Neville and Doreen Lawrence struggling through their tears was awful. The Met has come to know them well and I have enormous respect for their quiet dignity and powerful determination to see justice, which I share.

"I cannot rewrite history and the events of the past but I do have a responsibility to ensure the trust and the confidence of the people of London in the Met now and in the future. This will need a considered response to meet head-on the concerns that have been expressed in yesterday's report."

Ellison's report damaged the Met's reputation, which was already tarnished by Plebgate.

Theresa May branded the revelations about the Lawrence case, some 21 years after the murder, as "profoundly shocking and disturbing", adding that "policing stands damaged today". She said the full truth had yet to emerge.

Ellison found that during the 1998 Macpherson inquiry into the Lawrence case the Met had a spy in the Lawrence camp.

On Friday, Condon denied authorising undercover police officers to target the Lawrence family.

Condon, Met commissioner from 1993 to 2000 and now a peer, said in the House of Lords: "I have read the reports by Mark Ellison QC and Chief Constable Creedon and I am in broad agreement with their findings. I also fully support the further action outlined by the home secretary.

"I confirm and restate the comments I made in the House of Lords last month. That at no stage did I ever authorise, or encourage, or know about any action by any undercover officer in relation to Mr and Mrs Lawrence or their friends or supporters or the Macpherson inquiry hearings. Had I known I would have stopped this action immediately as inappropriate.

"I made this statement in the House of Lords because for me it is the equivalent of saying it on oath and I am aware of the full consequences of any attempt to mislead the House of Lords.

"Similarly I always wished the Macpherson inquiry to have full access to all relevant information and documents held by the MPS and was dismayed and saddened to read the findings about the alleged withholding of information.

"I will continue to do all in my power to support the ongoing investigations into these matters. And I realise the enormous anxiety and concern that these fresh allegations will generate with Mr and Mrs Lawrence and their supporters."