Scotland Yard said Sir Ian wrote to the Home Office permanent secretary, John Gieve, to ensure the terrorist investigation took precedence over any Independent Police Complaints Commission (IPCC) investigation.
Later the same day, the Metropolitan Police agreed to hand over the investigation to the IPCC.
Scotland Yard said last night that the letter, which was also sent to the IPCC, was "to clarify the role of IPCC if, as it then appeared, the shooting at Stockwell tube station involved a suicide bomber who had been involved in the previous day's incidents".
It was reported last night that Sir Ian was concerned about the possible security risk posed by an independent inquiry.
Mr de Menezes' legal team accused police of breaching their statutory duty yesterday by not immediately inviting the IPPC to start its inquiry. The family's lawyer, Harriet Wistrich, called for Sir Ian to resign. She is meeting IPCC representatives for the first time today.
With pressure growing for a public inquiry into the shooting after further details emerged of blunders in the police operation, Scotland Yard is also facing increasing criticism over their "shoot-to-kill" policy.
Former Cabinet minister Frank Dobson last night said that Sir Ian's position was "very difficult" because he was partly responsible for people being misled, including Prime Minister Tony Blair. "The public and everyone had been misled by the police not correcting the story that first came out," he told BBC2's Newsnight.
Leaked documents, believed to be from the IPCC inquiry suggest Mr de Menezes was sitting calmly in the Tube carriage, surrounded by surveillance officers, moments before police stormed in and fired eight bullets into him.
According to the documents, an officer grabbed Mr de Menezes, pinned his arms down, and pushed him back on a seat before he was shot. Mr de Menezes's cousin, Alex Alvez Pereira, said: "The officers who have done this have to be sent to jail for life because it's murder and the people who gave them the order to shoot must be punished."
According to a statement in the leaked report, one of the surveillance officers, codenamed Hotel Three, saw four firearms officers approaching the suspect at Stockwell station.
The witness statement said at least three surveillance officers were positioned. "I immediately identified these men as police [firearms] officers probably from SO19 and decided to identify the male in the denim jacket who I followed on to the Tube to them as they appeared to be looking into the carriage as if searching for someone."
Hotel Three stood up and walked to the carriage doors. "I placed my left foot against the open carriage door to prevent it shutting ... I shouted 'He's here' and indicated to the male in the denim jacket with my right hand. I then heard shouting which included the word 'police' and turned to face the male in the denim jacket."
The officer said Mr de Menezes then stood up and walked to within a few feet of him. "I grabbed the male in the denim jacket by wrapping both my arms around his torso pinning his arms to his side. I then pushed him back on to the seat where he had previously been sitting ... I then heard a gunshot very close to my ear and was dragged away on to the floor of the carriage." Mr de Menezes was shot eight times, seven times in the head, once in the shoulder. Three bullets missed him.
Statements from witnesses had said earlier that Mr de Menezes was followed from his flat in Tulse Hill on to the bus that took him to Stockwell station.
Mr de Menezes was mistakenly believed to be linked to the men who tried to detonate bombs in the failed July 21 attacks. Contrary to earlier police and witness statements he was not wearing a heavy jacket and did not run on to the platform.
The documents also reveal details of what officers describe as a " training camp" in north Wales linked to a suspected bomber. The " training camp" in the Cambrian mountains in north Wales is understood to have been used by some of the July 21 suspects for "bonding" sessions.
According to the material, obtained by ITV News, officers are investigating a possible link between the camp and Lampeter University. The university has an Islamic studies centre.
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