Anger over the geisha-inspired spread comes just days after Vogue earned social media wrath for the March issue's cover image featuring a clutch of now popular young models.
On Wednesday, Kloss responded to the backlash with a statement on Twitter, saying she was "truly sorry for participating" in the photoshoot.
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This isn't the first time that the fashion outlet has been criticized for featuring racial stereotypes and appropriating culture; in the past, they've caught heat for invoking orientalism at the 2015 China-themed Met Gala to French Vogue's use of blackface for a shoot.
Critics are lobbing charges of whitewashing and cultural appropriation against Vogue, joining the rampant online criticism of the magazine for colourism and tokenism in its already maligned March issue.
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One photo shows her on the stairs of a tea house while in another, she stands next to a sumo wrestler.
Some took issue with Kloss's inclusion in this shoot for a diversity issue.
"My goal is, and always will be, to empower and inspire women", she said.
So, upon seeing the images of supermodel Karlie Kloss wearing a black wig and "doing geisha things", it didn't take long for people to really start going in. "I will ensure that my future shoots and projects reflect that mission".
Photographer Mikael Jansson shot the editorial in Japan, reportedly as an homage to a 1966 Vogue shoot by Richard Avedon of German model Veruschka. During the 2012 Victoria's Secret Fashion Show, the 24-year-old wore a Native American-inspired headdress and matching outfit.