"The Metropolitan Police Service initially resisted us taking on the investigation, but we overcame that," said John Wadham, chairman of the Independent Police Complaints Commission (IPCC).
But Sir Ian Blair, the director of London's Metropolitan Police, denied allegations of a cover-up.
The IPCC is now investigating the killing of Jean Charles de Menezes, who police shot in the head eight times on an underground train in south London.
Wadham's statement was issued after lawyers for the Menezes family met the IPCC, demanding more information about the killing.
Kept from scene
Menezes, 27, was shot and killed by police who tailed him to the underground station on 22 July, one day after four bombs had been carried onto London's transit system.
The bombs failed to detonate fully. Two weeks earlier, 52 commuters had been killed after four bombers struck London trains and a bus in the British capital.
"The Metropolitan Police Service initially resisted us taking on the investigation, but we overcame that"
John Wadham, Independent Police Complaints Commission
The Guardian newspaper reported on Thursday that police kept the IPCC away from the scene of the shooting for three days.
A spokeswoman for the commission declined to say if that delay was unusual.
The Home Office, which oversees national security in Britain, refused to comment.
Blair, under pressure to resign for attempting to scuttle the independent investigation, said: "This is not a cover-up."
In an interview with London's Evening Standard newspaper,
Blair said: "Those allegations, I have to say, do strike at the integrity of this office and the integrity of the Metropolitan Police and I fundamentally reject them."
The police chief also denied trying to block an independent inquiry, saying that it was vital to continue with the counter-terrorism investigation.
Menezes, who was wearing a light
denim jacket, was shot eight times
On Tuesday and Wednesday, ITV News leaked documents from the official complaints commission investigation that contradicted police accounts of Menezes' death.
That prompted Jenny Jones, an official at the Metropolitan
Police Authority, the watchdog for London's police force, to say the investigation must be made public.
Call for transparency
"The leaks, apparently from the IPCC report, demonstrate that there are problems with the procedure. I therefore think it's time now to come clean and actually let us all know exactly what's been going on," Jones said on Thursday.
"The Met has a fantastic reputation... But we have to find out what went wrong in this surveillance operation and whether the bad information we have received about it was an accident or a cover-up," said Jones, a member of the opposition Green Party.
On Thursday, lawyers for the Menezes family demanded answers amid the allegations of a police cover-up.
"Those allegations, I have to say, do strike at the integrity of this office and the integrity of the Metropolitan Police and I fundamentally reject them"
Sir Ian Blair, director,
London Metropolitan Police
"This has been a chaotic mess," said lawyer Gareth Peirce. "One of the things we asked the IPCC to investigate is: 'Are there lies that have been told? Who told them?'"
In the heightened state of anxiety following the failed attack on 21 July, witnesses reported that Menezes, who they said was acting suspiciously, jumped over station ticket barriers before bolting towards a train.
Blair eventually apologised for the killing. However, on 22 July, he had told journalists that Menezes failed to obey their instructions.
The leaked reports made by public by ITV News, however, suggested officers trailed Menezes for more than a half-hour and made no attempt to stop him.
The surveillance officer who called in reports about Menezes described him as wearing a light denim jacket - instead of a heavy coat capable of concealing a bomb initially reported - and carrying nothing, but suggested it was "worth someone else having a look".
The Brazilian calmly entered the Stockwell underground station, paused to pick up a free newspaper and used his travel card to pass through the barriers, according to the ITV report, citing documents apparently based on closed-circuit
"The Met has a fantastic reputation... But we have to find out what went wrong in this surveillance operation and whether the bad information we have received about it was an accident or a cover-up"
Jenny Jones, Metropolitan Police Authority official and member of the opposition Green Party
After descending the escalator and running to catch his train, Menezes took a seat in the carriage and was pointed out to armed police by one of at least three surveillance officers who had followed him onto the train.
The surveillance officer says he then "heard shouting which included the word 'police'", ITV reported.
Menezes stood up and walked towards the surveillance officer, who tackled Menezes and pushed him back into the seat, then "I heard a gunshot very close to my ear and was dragged away on to the floor", the officer said.
The BBC and Sky News, citing unidentified sources, reported on Thursday that a secretarial staff member of the complaints commission had been suspended over the leaked information.
The commission refused to comment on the reports.