The retail group has reacted negatively to Ocean's decision to release his album via iTunes a week early, when it was previously scheduled for a July 17 release.
Ocean's manager Christian Clancy tweeted about Target's ban: "Target has refused to carry Frank's album because of iTunes exclusive. Interesting since they also donate to non-equal rights organizations."
In a statement to MTV News, Target said: "At Target, we focus on offering our guests a wide assortment of physical CDs, so our selection of new releases is dedicated to physical CDs rather than titles that are released digitally in advance of the street date."
They added: "The claims made about Target's decision to not carry the Frank Ocean album are absolutely false. Target supports inclusivity and diversity in every aspect of our business. Our assortment decisions are based on a number of factors, including guest demand.
"Target has a longstanding tradition of supporting music and artistry that reflects the diverse landscape of American culture. Our history of partnering with diverse artists includes recent partnerships with a variety of musicians, such as Ricky Martin, B.o.B., and Gloria Estefan."
Clancy later took to Twitter to delete his original message and downplay his comment, saying: "Note to self: Take your own advice. Emotional knee-jerk reacting isn't the move."
Frank Ocean has risen to the top of the iTunes album chart since the record was released on Monday.
Watch the music video for Frank Ocean's latest single 'Thinkin Bout You' below: