The statue, which was installed in 2008, will be removed on Thursday, said local authority Bournemouth, Christchurch and Poole (BCP) Council in a statement.
"We acknowledge the differing views of the life activities of Baden-Powell and want to create time for all views to be aired, and to minimise the risk of any public disorder or antisocial behaviour that could arise were the statue to remain in situ," it said.
The Dorset County Scouts group supports the removal, the council added.
Vikki Slade, BCP council leader, called for discussions on the future of the statue.
"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," she said in a statement.
Slade also addressed the move in a Facebook post on Wednesday.
"I do not wish to see the statue removed," she wrote. "However we have had police advice that this statue is on a target list for attack and due to its proximity to the water and its delicate and historic nature I was asked to approve its temporary removal."
The move is part of a wave of actions against monuments glorifying the UK's colonial history.
On Sunday, protesters in Bristol tore down a statue of slave trader Edward Colston and dumped it into a river, and local authorities in east London removed a statue of slave owner Robert Milligan on Tuesday.
Who was Baden-Powell?
Robert Stephenson Smyth Baden-Powell, 1st Baron Baden-Powell of Gilwell, was born February 22, 1857 in London and died January 8, 1941 in Nyeri, Kenya, according to encyclopedia Britannica.
He was revered as a national hero for his actions as a British Army officer in the South African War (1899-1902), and went on to found the Boy Scouts in 1908. Two years later, he co-founded the Girl Guides, a similar organization for girls.
The Scouts is aimed at boys aged between 10 and 14 years old. The organization says scouting "exists to actively engage and support young people in their personal development, empowering them to make a positive contribution to society."
Baden-Powell developed an interest in teaching young people when he found out his 1899 military textbook "Aids to Scouting" was being used for training boys in woodcraft.
He decided to set up a trial camp for boys on Brownsea Island, near Poole, in 1907, and then wrote a book for what he called the Boy Scout movement.
Before long there were Scout troops popping up across Britain, and Baden-Powell published a book called "Scouting for Boys" in 1908.
Two years later Baden-Powell retired from his army position to concentrate on the Scouts, and founded the Girl Guides with his sister Agnes that same year.
Why was he controversial?
Critics of Baden-Powell say that he held homophobic and racist views, and sympathized with fascists like Adolf Hitler and Benito Mussolini.
Former Bournemouth East Labour parliamentary candidate Corrie Drew told BBC Breakfast television Thursday: "A quick look into his history shows that he was very open about his views against homosexuality and that he was a very open supporter of Hitler and of fascism and quite a strong, outspoken racist."
She said: "We can't just excuse people's shocking values because they were in the past," adding: "We can commemorate the positive work without commemorating the man."
Drew added that the statue is not historic -- it has only been there for about a decade. "It's not part of our history in itself," she said.
However, some local politicians have spoken out in defense of the statue.
Robert Syms, MP for Poole, wrote on Twitter: "For the avoidance of doubt I am opposed to the permanent removal of the statue of Baden-Powell from Poole Quay."
Conor Burns, MP for nearby Bournemouth West, called on BCP Council to put the statue back.
"The removal of the statue of Lord Baden Powell from Poole is a huge error of judgement," he tweeted.
On Thursday morning locals in Poole gathered to show their support for the statue.