The so-called police "shoot to kill" policy did not plan for the events that led to the shooting of an innocent Brazilian, says one of its architects.
Mr Menezes was shot seven times in the head on a Tube train
It was not prepared for an intelligence gathering operation turning into a live and mobile threat, Chief Constable Barbara Wilding told BBC's Panorama.
She headed the Metropolitan Police working party that drew up the policy following the 11 September attacks.
Jean Charles de Menezes was shot after being mistaken for a bomb suspect.
He was shot seven times in the head at Stockwell Tube station in London the day after the failed 21 July bombings.
Chief Constable Wilding, now chief constable of South Wales, told Panorama that procedures for preventing suicide bombings - called Operation Kratos - dealt with two restricted scenarios:
Mr Menezes was mistaken for a suicide bomb suspect and killed after being followed by police who saw him leave a block of flats being staked out in connection with the 21 July failed attacks.
Chief Constable Wilding told Panorama: "The planning that we did, did we look at a mobile intelligence gathering operation going live? The answer is no we didn't."
The Met's Assistant Chief Commissioner Steve House said Operation Kratos would be kept in place and constantly refined.
"We will seek any improvements that we can, both in the equipment and in the tactics, to make sure that it is the most effective deterrent that we have to suspected suicide terrorists coming to London again," he said.
The Panorama investigation also found that the radios used by the officers who shot Mr Menezes did not work deep underground in Stockwell Tube station.
Former Metropolitan Police Commissioner Lord Stevens said the problem had been repeatedly raised with the Home Office in the past.
"Communications are essential and the reason for that is, in a fast-moving situation, you have to inform the officers involved what is taking place," Lord Stevens said.
"Equally importantly they have to get back in touch with you."
The programme also found that the policy, called Operation Kratos, did not require police to see a "suicide jacket" before opening fire - that possession of intelligence that a person was a threat was enough.
Panorama found that contrasted with the policy of Israeli police, who the Metropolitan Police had consulted on suicide bombers.
Major General Mickey Levy, the police commander in Jerusalem between 2000 and 2004, told Panorama that Israeli officers had to be sure a person was carrying a suicide belt or bomb before taking action.
This special edition of Panorama will be broadcast on Wednesday 8 March at 2100 GMT on BBC One.