Police have launched an investigation after an intruder gained access to the site of the historic castle in the early hours of November 6 before stealing the keys.
The keys gave access to the tower's drawbridges as well as conference rooms and a restaurant, according to a statement from Historic Royal Palaces, the charity that runs the site.
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
The intruder was stopped and taken off the site, but afterwards it was found that the keys were missing.
A spokeswoman said the Crown Jewels, which include priceless crowns and sceptres used by Queen Elizabeth II on ceremonial occasions, were never at risk of being stolen.
"The intruder did not gain access into the Tower itself," the Historic Royal Palaces spokeswoman said.
"He did manage to get round the gate at the main entrance but was then apprehended and escorted off the premises.
"At no point was the security of the Tower at risk."
Historic Royal Palaces said in a statement: "It would not have been possible to gain access to the Tower with any of these keys. All the affected locks were immediately changed.
"We have carried out an internal investigation and have concluded that our well-established security systems and procedures are robust.
"However on this occasion, these procedures were not carried out to the expected standard. A staff disciplinary procedure is underway to address this issue."
A Scotland Yard spokesman said: "An allegation of theft has been made to police, which is being investigated."
