Last night it was not clear who was responsible for the blunders as security firm G4S said it did not handle master keys.
Sources said staff at Wembley noticed the keys were missing last Tuesday after a routine check.
Their colleagues made a similar discovery at Wimbledon on Friday evening as the venue went into lockdown for the Games.
One said: "They quickly realised it was a big deal and called the Met in who sent search teams to try and track them down. But they couldn't turn anything up.
"To say it is the mother of all cock-ups is an understatement. The officers are furious their time has been wasted in this way.
"These were hi-tech laser keys which cost anything up to £40,000 a set as they cannot be copied. They are the same type as you get at prisons."
A spokesman for G4S said: "We have no record of losing any keys. G4S does not have sole possession of any important sets of keys.
"The managers of security at venues are employed by Locog."
But G4S has been plagued by scandal ever since it was awarded the government contract worth £284million to provide private security for the 2012 Olympic Games.
The fiascos have threatened to end the reign of the company's controversial chief executive Nick Buckles.
Thousands of military personnel and hundreds of police officers had to be parachuted in to take over Olympic security at the 11th hour after the firm admitted it could not provide its full quota of 10,000 fully trained guards.
Hundreds of G4S security staff have failed to turn up for work at important Olympic sites across the country. And two suspected illegal immigrants were employed by G4S sub-contractor, East Midlands Security, as Olympic guards.
A Met spokesman said: "At 12.30pm last Tuesday police were alerted to the loss of keys at Wembley Stadium.
"Officers attended the venue to assist in the search for the missing items but nothing was found.
"Detectives also went to ascertain if there was any evidence of criminal offences, however at that time there were none."
Last night senior sources blamed G4S for losing a similar set of keys during the Wimbledon Championships, sparking a similar security nightmare. One said important keys, including a set controlling access to several secure locations and the drugs safe, were mislaid.
- DAILY MAIL
