Officers searching the stadium in London ahead of the start of the Games misplaced the keys, prompting an investigation by Scotland Yard, but organisers insisted that security has not been compromised.
Organisers stressed that the keys were for internal doors and the relevant locks have now been changed.
Scotland Yard is not treating the incident as a criminal matter.
A Metropolitan Police spokeswoman said: “On the morning of Tuesday 24 July officers on Olympic police operations at Wembley stadium reported that internal security keys, being used by them as part of searches, were missing.”
She said officers searched the stadium but could not find the keys.
“Detectives also attended to ascertain if there was any evidence of criminal offences,” the spokeswoman said. “There’s none at this time.”
She added: “There is absolutely no security concern in relation to the stadium as measures were taken immediately to secure all key areas of the venue.”
A spokesman for London 2012 dismissed fears that security had been breached.
“These were internal keys, locks have been changed and the security of the venue has not been compromised in any way,” he said.
Wembley, England’s national stadium, is one of six venues being used for the football tournament and hosted Great Britain men’s 3-1 victory over the United Arab Emirates on Sunday.
Both gold medal matches will be played there.