Statues of historical figures Robert Milligan and Robert Baden-Powell have reportedly been removed on public safety grounds.
The owner of the land where the monument of slave owner Milligan stood at West India Quay in east London told The Times that the council were informed Black Lives Matter protesters might attempt to topple the statue themselves.
It was taken away from its plinth on Tuesday evening and is currently being stored at a secret location.
The move comes after a statue of 17th-century slave trader Edward Colston was thrown into Bristol harbour during a Black Lives Matter protest over the weekend.
Bournemouth, Christchurch and Poole Council said it also planned to temporarily remove a statue of Scouts founder Robert Baden-Powell from Poole Quay on Thursday over concerns it may be targeted by protesters.
The council said it wanted to "minimise the risk of any public disorder or anti-social behaviour that could arise were the statue to remain in situ" while views on Lord Baden-Powell are shared.
Council leader Vikki Slade said in a statement issued on Wednesday: "Whilst famed for the creation of the Scouts, we also recognise that there are some aspects of Robert Baden-Powell's life that are considered less worthy of commemoration.
"Therefore, we are removing the statue so that we can properly involve all relevant communities and groups in discussions about its future, including whether a more educational presentation of his life in a different setting might be more appropriate.”
Slade said on Twitter that the decision was taken following a "threat", adding: "It's literally less than three metres from the sea so is at huge risk.”
The statue was installed in 2008 and faces Brownsea Island in Poole Harbour, where the Scout movement was started by Baden-Powell.
The council said it would be "put into safe storage" and that Dorset County Scouts "have been advised and support the position".
Anti-racism campaigners have compiled a list of monuments they want removed – including Nelson’s Column.
A statue of Queen Victoria in Leeds was also defaced with the words “racist”, “slave owner” and “Black Lives Matter”.
The Topple the Racists website, which says it was set up by an anti-Donald Trump campaign, has listed a number of sites across the UK involving historical figures where it says there is “responsibility for colonial violence”.
The statue of Colston was ripped from its plinth and thrown into Bristol harbour on Sunday.
The Colston statue has since been lifted out of the water and taken to a secure location before it becomes part of a museum collection, Bristol City Council said.
In 2010, declassified MI5 files revealed that Lord Baden-Powell was invited to meet Adolf Hitler after holding friendly talks about forming closer ties with the Hitler Youth.
An online petition to "defend Poole's Lord Baden-Powell statue" has received more than 3,500 signatures.