The disclosure, in a report by the Independent Police Complaints Commission, puts fresh pressure on Sir Ian Blair, the Commissioner of the Metropolitan Police, and his officers over the shooting.

Mr de Menezes, 27, was shot seven times in the head by a firearms team on a train at Stockwell Underground station on July 22 last year as police hunted for terrorists who had tried to attack the London transport system the day before.

Police sources say that the report, which is being studied by the Crown Prosecution Service, shows that a Special Branch logbook describing Mr de Menezes’s last movements had been altered to hide that he had wrongly been identified as a suspect.

Mr de Menezes was shadowed by a Special Branch team as he headed to Stockwell station. They believed that they were following a deadly attacker and radioed another officer with reports on what was happening. He kept a log.

One of the team identified Mr de Menezes as the terrorist suspect. This was noted, although the IPCC also found that elsewhere in the log there were “degrees of doubt” raised by the team.

The log was changed at a debriefing meeting at 8pm that night, about ten hours after the shooting. Police were still saying that Mr de Menezes might have terrorist links.

The log originally said that there was a positive identification but the word “not” was then added. None of the radio traffic during the operation was recorded, which meant that blame for the events leading to Mr de Menezes’s death could have fallen on the commanders and controllers rather than the team.

The IPCC team is said to have been alerted by a whistle-blower. A scientific technique for checking changes in documents showed the change that had been made. The team has denied changing the log.

Later that night the Anti- Terrorist Branch SO13 finally cleared Mr de Menezes but the IPCC found that the Commissioner was not told until 10.30am the next morning, more than 24 hours after the death. The delay will raise more questions about the handling of the operation and its tragic conclusion and why Sir Ian was left in ignorance for so long.

The report is said to make uncomfortable reading for police, drawing attention to a string of errors. There are questions not only about identification but also communications, what orders were issued and by whom, and who did what.

Mr de Menezes’s family last night called for Sir Ian to reconsider his position in light of the disclosure.

“It seems that Sir Ian Blair was not aware of any of this information for quite a while following Jean’s death, which does raise certain questions about how in touch he was with the operation,” Asad Rehman, a spokesman for the family, said. “Sir Ian Blair is ultimately responsible for the safety of people in London and this country. It seems he didn’t have his eye on the ball.”

Ten officers have been named in the IPCC report as facing possible charges. They include a senior officer, a middle-ranking officer and junior officers involved in the operation.

The most senior is Commander Cressida Dick, the officer empowered to order officers to open fire under the rules of Operation Kratos, a special set of rules for dealing with the threat from suicide bombers. She denies that she gave the key codeword.

Yesterday the IPCC refused to comment on the report, which has been with the CPS for ten days and is now being examined with a file of evidence by counsel.

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