BRAZIL'S deputy attorney general and a senior official from Brazil's ministry of justice will tomorrow morning hold discussions in London with members of the Independent Police Complaints Commission, the Metropolitan Police and senior officials from the Foreign Office. Despite the diplomatic manners that will initially be on show, a Foreign Office source hinted that this will be an "uncomfortable" gathering. It could be very uncomfortable.

On July 22, an innocent Brazilian citizen was gunned down inside a London Underground train during a bungled police operation which followed the second terrorist attack in London. The Metropolitan Police says the shooting was a "tragic mistake".

But behind the public contrition there lies a web of contradictory statements, deviation from routine procedures, and a mist of confusion that has led to serial calls for the resignation of the Met's head, Sir Ian Blair.

And throughout four weeks of calls for clarity and the truth, has been the odour of a police cover-up that has refused to retreat in its intensity.

The two Brazilian officials, Wagner Goncalves and Marcio Pereira Pinto Garcia, will, above all, be seeking assurances that every detail of the death of Jean Charles de Menezes will be investigated and that they are kept informed. On that basic request the two Brazilians may be disappointed.

The IPCC has already hinted that the Brazilians will be told no more than lawyers from the de Menezes family.

The two Brazilians are likely to leave the meeting with the realisation that they may need to be patient in their desire to know the full facts. It could be two years and more before the IPCC publishes its findings. Its report will need to be sent to the official coroner. It will also have to be examined by lawyers at the Crown Prosecution Service. A formal inquest will take place and if there is any prosecution of any officer involved, that will take precedence over the report's publication. The Home Secretary, if he believes any part of the IPCC's report compromises national security, could also order an edited version to be made public, with key elements remaining confidential.

That is a lengthy period for a climate of cover-up to endure and Sir Ian Blair knows it. In an interview with the BBC, given at the end of last week, the Met chief said: "Of all the allegations made in the last couple of weeks, the matter I would most want to reject is the concept of a cover-up . . . tragic as the death of Mr Menezes is, and we have apologised for it and we take responsibility for it, it is one death out of 57."

The Met is currently involved in the largest criminal inquiry in England's history, centred on the people who lost their lives in the terrorist attack in London on July 7. There are double that number whose lives have been wrecked by the horrors of the attack carried out by four suicide bombers.

Yet despite Sir Ian's plea that "we cannot let one tragic death outweigh all the others", the confusion and chaos surrounding the shooting of de Menezes has forced Britain's senior police officers last Friday to question the use of the shoot-to-kill policy that led to an innocent death.

"Operation Kratos" was the codename for the police policy that gave authority to armed officers from the SO19 firearms squad to kill a suspected suicide bomber if deemed necessary. A suspected suicide bomber would not be targeted with a shot to the body - a shot likely to trigger explosives strapped to a bomber.

If a suspect was targeted there would be a lethal shot to the head.

But how did de Menezes get to the point where he was identified, wrongly, as that kind of risk?

Two weeks after the first attacks on July 7 London's transport network was hit by a second wave of attacks. No bombs were detonated on July 21 and a massive manhunt for four bombers was launched.

Police are said to have quickly established the identity of some of the men they were looking for and began monitoring a flat in Scotia Road, Tulse Hill, in south London.

The address they believed was linked to the second wave of attacks.

A police surveillance team believed two of the suspected bombers lived in the block, one of them, Hussein Osman. Among the surveillance team in Scotia Road was a soldier from a new "special forces" regiment that had only become operational in April. The Special Reconnaissance Regiment (SRR) is the first special forces unit to be created in the UK since the end of the second world war. The SRR is based in Hereford, its personnel selected and trained by the SAS.

Geoff Hoon, then defence secretary, announced on April 5 in a written Commons answer that "the pursuit of international terrorists" would be the SRR's priority.

However, the involvement of the SRR in the operation on July 22 was not confined to just one soldier at Scotia Road. According to security sources, SRR personnel were involved in the tailing operation that saw de Menezes leave the block of flats, board a bus, and then enter the tube station at Stockwell. SRR personnel are also believed to have been on the tube train when he was shot.

The SRR soldier at Scotia Road (given the codename Tango 10) used equipment which sent realtime pictures of all who came and went from the flats. Those receiving the pictures could check them against footage of who they were looking for. One security source said: "In this kind of operation you never leave. You need to pee: you use a bottle; if there's no bottle, tough. You never leave."

The police account says there is no footage of de Menezes leaving because the SRR soldier had to relieve himself. The police account says he sent out a message calling the man who left [de Menezes] an "ICI" - a white northern European. It was also suggested that "it would be worth someone else having a look".

Hussein Osman - arrested in Rome and scheduled for deportation to the UK within the next two months - was not an ICI. The CCTV footage of Osman the police held showed an Asian/north African male.

De Menezes took a bus to Stockwell tube station, stopping briefly at Brixton. The surveillance operation logged his every step. An assessment was made on the basis of his demeanour: he was identified as a suspect. By whom? That is still unclear. It is also understood that the senior police officer in charge of the operation, Commander Cressida Dick, had ordered de Menezes at this stage to be detained before he went into the tube station and that he should be alive.

So why was de Menezes not stopped before the station? Suggestions that SO19 officers had yet to arrive in the vicinity of the station are irrelevant if armed SRR personnel were part of the surveillance team tracking the 27-year-old Brazilian.

Details contained in a leaked IPCC draft report given to ITV News last week reveal that the Brazilian walked into the station lobby, picked up a free newspaper, used a travelcard at the ticket barriers, and headed towards the train. Three members of the surveillance team followed de Menezes on to the train and sat alongside him. Another sat near the train's doors.

The leaked IPCC report says the surveillance team inside the train saw four other armed personnel (said to be from SO19) moving along the platform. The IPCC report says one of the surveillance team - codenamed called Hotel Three - saw the men on the platform, and said they were "probably" - but not definitely - "from SO19". He said he decided to identify the male in the denim jacket [de Menezes] to them. "I placed my foot against the open carriage to prevent it shutting . . . I shouted, 'He's here, ' and indicated to the male in the denim jacket with my right hand. I heard them shouting which indicated the word 'police' and turned to face the male in the denim jacket." The IPCC account says de Menezes stood up and walked towards the armed men. "Hotel Three" decided to intervene.

The report says he wrapped his arms around the young Brazilian and pushed him back into his seat.

Hotel Three says he then heard a gunshot close to his ear and he was dragged away on the floor of the train carriage. The report also says that one of the officers from SO19 shot de Menezes seven times in the head and once in the neck. Three other shots were fired and missed.

A security agency source contacted by the Sunday Herald said: "This takeout is the signature of a special forces operation. It is not the way the police usually do things. We know members of SO19 have been receiving training from the SAS, but even so, this has special forces written all over it."

The IPCC report offers a degree of clarity absent in the "eyewitness" accounts which suggested the suspect had been wearing a padded jacket and had vaulted a ticket barrier.

These accounts are governed not by rational recall but by panic. They reflect public terror and fear. But despite Sir Ian Blair's insistence that "there was no evidence" that the Met had made up or leaked stories suggesting that the victim was running from the police and had been wearing a bulky jacket and had jumped over a barrier, the initial postmortem report into de Menezes's death states the young Brazilian had "vaulted over the ticket barrier".

A post-mortem report does not take its information from media reports. The police are contacted directly and written accounts are delivered. Details of the barrier being "vaulted" therefore came from the police. Why?

And why at 4pm - five hours after the shooting - when the police would have known they had not killed Hussein Osman but a young Brazilian, did Sir Ian hold a press conference and insist that the shooting was "directly linked" to the anti-terrorist operation?

It took until 5pm the following day, July 23, for Scotland Yard to formally admit that the victim was not linked to the anti-terrorism operation. At 9.30pm Scotland Yard issued the name Jean Charles de Menezes.

However, the day before the admission that there was no anti-terrorism link, Sir Ian wrote to John Gieve, the permanent secretary at the Home Office, arguing that an internal inquiry into the killing should take precedence over an independent investigation. But why was Ian Blair worried that an IPCC investigation could impact on security and intelligence? Was he concerned that it was not just his force's officers, but also the personnel of the new special forces regiment, the SRR, who would be exposed? He told Gieve that he feared the IPCC would have to inform the family of everything that was found - and "this investigation involves secret intelligence". It was also believed that any outside investigation could damage the morale of SO19.

Despite the Met chief 's plea, he was over-ruled. The IPCC was brought in. But no explanation has so far been offered as to why it took a further three days for the IPCC investigation team to be given access to the scene of the shooting at Stockwell. In normal procedures, an IPCC team would have been given access "within hours" to preserve evidence.

Despite Sir Ian's insistence that the Met "do not spin", the contradictions and confusion point either to a cover-up designed to protect what the Met still believes is valued intelligence material, or to a confused chain of command between police and the clear involvement of special forces personnel from the new Special Reconnaissance Regiment.

De Menezes's cousin, Alessandro Pereira, certainly has no doubts that the police have not been forthcoming with the truth about the circumstances surrounding the shooting.

"For three weeks we have listened to lie after lie about Jean and about how he was killed, " he said. "I want Ian Blair to think how it felt having to ring Jean's mother and father . . . and tell them their son was dead, that he was killed in such a way. The police know Jean was innocent and yet they let my family suffer."

This was the SRR's first public test of their operational skills in combating terrorism. It would be highly damaging for the government if a new unit, designed to increase national protection, were found to be incapable of working successfully alongside special armed units of the Met. A full and open public inquiry would answer such questions, but it would also expose a special forces unit to public scrutiny, something the SAS has been able to resist throughout its history.

Like the two Brazilian justice officials expecting answers tomorrow, we may all have to wait much longer for a believable account that helps explain the death of Jean Charles de Menezes.