Conde Nast's executive vice president James Woolhouse sent the message on Monday.
He told "country presidents" of magazine titles that any photography shoots by Richardson that had already taken place, but not been published, should be replaced with other images.
He wrote: "I am writing to you on an important matter. Condé Nast would like to no longer work with the photographer Terry Richardson.
"Any shoots that have been commission(ed) or any shoots that have been completed but not yet published, should be killed and substituted with other material.
"Please could you confirm that this policy will be actioned in your market effective immediately. Thank you for your support in this matter."
Richardson is known for his sexually explicit photo shoots of stars including Kylie Jenner, who had a calendar shot by him.
He's also directed videos like Miley Cyrus's Wrecking Ball and Beyonce's XO.
In 2014, the 52-year-old wrote an article for The Huffington Post in response to the "internet gossip and false accusations" against him.
He wrote that sexual imagery formed a part of his photography, adding: "I have never used an offer of work or a threat of rebuke to coerce someone into something that they did not want to do."
Richardson also referred to a 2004 gallery show which "depicted sexual situations", saying he "collaborated with consenting adult women who were fully aware of the nature of the work".
Terry has photographed pretty much everyone. Is he an artist disguised as a pervert or vice versa?