President Julius Maada Bio called the toppling of the famed tree "a great loss to the nation" as crowds gathered to look at the wrecked trunk.
The "Cotton Tree" was the most important landmark in the west African country which was founded by freed US slaves.
It is said that when they arrived by boat in the late 1700s, they gathered under its branches to offer prayers before moving into their new home.
The tree went on to appear on the country's banknotes and be celebrated in children's nursery rhymes.
"It was regarded as a symbol of liberty and freedom by early settlers," the president wrote on Twitter.
"We have to see what we are going to do to make sure that we keep the history of this tree here," he told Reuters at the scene.
"I want to have a piece of this history wherever I find myself – at the state house, the museum or city hall."
Until the storm snapped its 70-metre-tall trunk near the base, the kapok tree stood in the middle of a roundabout in central Freetown, its highest branches reaching above the surrounding tower blocks.
Victor Tutu Rogers was one of the last people to see the tree standing when he passed it at about 9.40pm on Wednesday as the rain and wind intensified.
"I dashed round the cotton tree on my way from work because I feared the branches might fall," he said.
"Shortly after that there was a heavy lightning and I heard a heavy bang - the sound of the tree falling behind me."
On Thursday morning, diggers cleaned up the wreckage - a sprawling heap of broken branches and bright wood newly exposed to the air.
Nearby buildings and cars appeared to have been damaged during the fall although no injuries were reported.
Freetown's Chief Administrator, Festus Kallay, said the city held its annual thanksgiving under the landmark every November.
"The Freetown skyline will hardly be the same again."
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