The five-storey penis has generated plenty of discussion since it was unveiled last week.
“Keep your penis inside” reads the graffiti painted on top of the artwork.
The company which owns the building, and was apparently given no prior warning before the penis popped up, announced on Friday that they would cover up the painting after complaints from residents in the central Kungsholmen neighbourhood.
However, the graffiti appears to be a marketing stunt rather than a protest at the painting.
The text included the name of a Swedish underwear brand, Petters Underwear, apparently keen to capitalize on the viral fame of Stockholm's blue penis.
Local residents headed to the area over the weekend to catch a glimpse or an Instagram snap of the mural, which has made headlines across the country.
The penis, painted in the blue and yellow colours of the Swedish flag, is the creation of artist Carolina Falkholt, who said she hoped to stimulate discussion about sex with her art.
It was painted on a legal graffiti wall established in Stockholm by the art organization Kollektivet Livet, meaning there was no need to consult with residents before painting it.
Art usually remains on the walls for around six months before being replaced by a new piece, but the Kungsholmen penis will be erased prematurely due to a high number of complaints.
Stockholmers looking at the artwork. Photo: Anders Wiklund/TT