The work was apparently inspired by lockdown and the implications of the coronavirus pandemic.
Last night Transport for London said the images had been removed as they breached its strict “no graffiti” policy , prompting a backlash on social media.
However, the Standard can today reveal that the artwork was in fact erased by a cleaner who had no knowledge of its significance - possibly as far back as last Friday.
One source said: “When we saw the video, we started to look into it and spoke to the cleaners. It started to emerge that they had noticed some sort of ‘rat thing’ a few days ago and cleaned it off, as they should.
“It rather changes the aspect for anyone seeking to go down the route of accusing us of cultural vandalism.”
The video apparently shows Banksy in a white protective suit and mask spray-painting stencils of his famous rat drawings – one using a face mask as a parachute and another with hand-sanitiser – on the inside of a Tube carriage as it travels towards Baker Street.
When the doors open at Euston Square, the message “I get lockdown" can be seen in graffiti on the station walls. The Tube doors then shut to reveal the rest of the message: "But I get up again".
Chumbawamba's song Tubthumping - also known as I Get Knocked Down - plays as the doors touch together.
The video, on Banksy’s Instagram page, has been viewed more than three million times. Banksy posted the accompanying message: “If you don’t mask – you don’t get.”
A TfL spokesman said: “We appreciate the sentiment of encouraging people to wear face coverings, which the vast majority of customers on our transport network are doing.
“In this particular case, the work was removed some days ago due to our strict anti-graffiti policy. We’d like to offer Banksy the chance to do a new version of his message for our customers in a suitable location.”
The video begins with a laptop playing PA Video footage showing the Underground being deep cleaned in May.
Banksy - clad in a white boiler suit, mask, goggles, blue gloves and an orange hi-viz jacket with the message "stay safe" printed on it - climbs on board a train posing as a TfL worker.
The video shows him ushering a masked passenger to move back, before stencilling a rat using a blue face mask as a parachute.
Another rat has a blue mask over its face, while one holds a bottle of hand sanitiser.
There are two rats, one on each of the carriage's doors, looking at each other.
Banksy, from Bristol, has created a number of artworks during the coronavirus lockdown.
In April, he created a series of rats causing mayhem in his bathroom and posted the caption: "My wife hates it when I work from home."
Later that month, a large face mask was placed on his world-famous piece The Girl With The Pierced Eardrum on Bristol harbourside.
An artwork entitled Game Changer, showing an NHS nurse as a superhero toy, went on display at Southampton General Hospital in May.
In June, Banksy posted a piece inspired by Black Lives Matter with a caption, part of which read: "People of colour are being failed by the system."
The following day, a statue of slave trader Edward Colston was toppled by protesters in Bristol and thrown into the harbour during a Black Lives Matter march.
Banksy posted a sketch showing his idea for the empty plinth - retrieving the statue from the water, putting it back on the plinth with cables around its neck and life-size bronze statues of protesters pulling it down.
He finished the caption by stating: "A famous day commemorated.”