A Special Branch surveillance officer, named as Owen, is being investigated by the Independent Police Complaints Commission (IPCC) after removing a line from his notes claiming Deputy Assistant Commissioner Cressida Dick said the Brazilian could "run on to Tube as not carrying anything".

Owen, a supervisor in the operations room at Scotland Yard, said he altered his version of events more than two weeks into the inquest because it was "misleading" and not "relevant".

Mr de Menezes's mother, Maria Otone, who sat in court as Owen admitted altering his log, was said to be "in shock".

Mr de Menezes's brother, Giovani da Silva, said it was a "sickening cover-up", adding: "This latest cover-up only increases suspicion about what officers were doing that day and whether they are telling the truth. We remain determined to uncover the truth."

Home Secretary Jacqui Smith said she wanted the IPCC to report "as quickly as possible".

She said: "This is a very serious matter which clearly must be investigated and the facts established. Once the facts are established we will decide, in consultation with the Metropolitan Police Authority, what further action may be necessary."

Owen said he altered his notes on October 7, and told a Scotland Yard solicitor what he had done the following day .

He told the jury at The Oval cricket ground, south London: "On reflection, I looked at that and thought I cannot actually say that."

He deleted more than he had intended because he was in a rush to get to an appointment, he claimed.

Saying he was now not sure who had actually said "let him run", he added: "All I can say was that one of the options was letting him run because he was not carrying anything and that there's a disagreement between management.

"I believe it was the commander but when I reflected I couldn't be sure, or whether she was saying this is what we are going to do, or this is one of the options. It was a woman's voice."

Minutes later, Ms Dick effectively directed the shooting of Mr de Menezes by ordering a "hard-stop", Owen added.

When asked if he was aware the changes to his notes were very serious, he added: "I have removed a line I believed was wrong and gave a totally false impression."

When asked if management had asked him to make that amendment, he replied: "No. I am sure of that, sir."

The full deleted line read: "CD – can run on to Tube as not carrying anything. Persuaded by U/I male amongst management."

His computer notes were not included in the Metropolitan Police's health and safety trial.

After retrieving the notes before the inquest, Owen said he "flicked through" them and saw there were a "few mistakes".

He explained: "The other thing I have done is delete the line I had identified as wrong and misleading when I did the statement."

When asked why, he replied: "The detail changes do not materially affect the statement."

Ms Dick previously claimed she believed Mr de Menezes posed a "great threat" as officers pursued him on July 22 2005.

The 27-year-old was killed by specialist firearms officers who mistook him for bombing suspect Hussain Osman after boarding a train at Stockwell Tube station.

The hearing continues.