“Much-loved” and “free-spirited” Merlina, who joined the flock at the Tower in 2007, has not been seen at her home in the 11th Century castle for several weeks.
Legend states that at least six ravens must be kept at the battlements or the kingdom of Britain will fall.
There are currently seven ravens in residence who are looked after by the Ravenmaster Christopher Skaife.
A spokesman for the Tower said: “Our much-loved raven Merlina has not been seen at the Tower for several weeks, and her continued absence indicates to us that she may have sadly passed away.
“Though it isn’t unusual for our ravens to roam outside the walls, free-spirited Merlina has previously always returned to the ravenmaster and his team, with whom she shared a wonderfully close bond.
"Merlina was our undisputed ruler of the roost, Queen of the Tower Ravens. She will be greatly missed by her fellow ravens, the ravenmaster, and all of us in the Tower community.”
Wild ravens live for 10 to 15 years. However, the Tower of London birds have been known to live until the age of 40.
Charles II is believed to have been the first monarch to officially decree that the birds must be kept at the stronghold at all times.
In the Second World War the ravens were used as spotters for bombs and planes during the Blitz.
When numbers fell to just a single raven guard, Winston Churchill ordered that the flock — known as an “unkindness” — be increased to at least six.
In 2018 the Tower launched a raven breeding programme after Historic Royal Palaces warned it was becoming “increasingly difficult” to source the birds and there were “very few legal captive raven breeders in the UK”.
Mr Skaife said he would be taking some time to mourn Merlina.
“I know so many of you lovely folk will be saddened by this news,” Mr Skaife said in a statement on social media.
“None more than me. Please excuse my absence for a few days.”
During the first lockdown the tourist attraction, which usually welcomed more than two million people each year, was shut and Tower staff became worried the birds were venturing outside the castle walls to forage.
Tower staff added that they had no immediate plans to replace Merlina.
“We now have seven ravens — one more than the required six, so we don’t have any immediate plans to fill Merlina’s vacancy.
“However in time we hope that a new chick from our breeding programme will be up to the formidable challenge of continuing her legacy."