Tower authorities started an internal investigation over claims that Moira Cameron - made the first female Beefeater in 2007 - was being bullied.
A statement said the allegations were being taken "very seriously" and that harassment was "totally unacceptable".
Beefeaters, officially yeoman warders, have guarded the Tower since 1485.
One of the warders involved in the probe has also received a caution from the Metropolitan Police for misuse of the internet.
Miss Cameron is the only woman among the 35 yeoman warders at the Tower of London.
The 44-year-old, from Argyll in Scotland, became the first female yeoman warder in the institution's history after completing the required 22 years of service in the Army.
'Close-knit community'
The statement from Tower of London said: "We can confirm that three yeoman warders are under investigation in response to allegations of harassment; two have been suspended.
"We take such allegations very seriously and our formal harassment policy makes it clear that this is totally unacceptable.
"We believe everyone is entitled to work in an environment free from any form of harassment, a principle that we expect all our staff to value and uphold.
"The Tower of London is a close-knit community and, understandably, this is a difficult time for us all."
 Yeoman wardens have guarded the Tower for more than 500 years |
The investigation is expected to conclude in two to three weeks.
A Metropolitan Police spokesman said: "A 56-year-old man received a caution under the Communications Act 2003 on Tuesday October 20 following an investigation by officers from Tower Hamlets.
"It related to inappropriate use of the internet."
The yeoman warders were appointed by Henry VII to guard the prisoners and attend the gates of the Tower.
Although their role is now mostly ceremonial, their duties include guarding the Tower and the Crown Jewels.
They also attend the coronation of the Sovereign, lying-in-state, the Lord Mayor's Show and other functions.
All the Beefeaters, who got their name because of their meat rations, live in flats in the Tower.
