The piece of street art - a red stop sign with three military drones on - was unveiled on the corner of Commercial Way, Peckham, on Friday.
But within an hour it was removed by a man with bolt cutters as witnesses took photos.
Police are treating it as theft. Officers are yet to make any arrests.
One gallery owner told the BBC the artwork could be worth up to £500,000.
Southwark Council's Jasmine Ali said she had every confidence they would get it back.
"We are not just talking about a street sign here, it is a work of art which was put there for the community. "It is street art and it is for the people," she said
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On Friday, one man described how he "watched in awe" as the sign was taken down at about 12:30 GMT.
Alex, 26, said no-one knew what to do and "we just watched it happen".
One man, carrying a banana, held a Lime bike steady for another, who reached up and cut the artwork free.
Wrenching it off the post, he then ran down the street and out of sight.
People looked on as the man took the artwork away
This is so weird to me like there was a crowd of people so entranced by the Banksy stencil but unable to intervene ??
Matthew Uden, managing director of the nearby funeral directors, said: "Having a piece of art by a famous street artist such as Banksy outside of our Camberwell branch was incredibly nice to see."
He said it was a shame it was no longer there.
You can literally remake it it's not that hard
Experts believe the location of Commercial Way and next to a funeral directors is significant to Banksy's latest work
Prof Paul Gough, vice-chancellor of Arts University Bournemouth, explained Banksy's work "always thrives on that ambiguity".
"He rarely puts art there by accident," Prof Gough said.
"There are some 40,000 comments on his Instagram - yet he follows nobody - and you get a whole range of interpretations."
