The New York band caused controversy when they released their EP back in 2006 as the cover features a black nanny with two white children - identified as a "mammy," a stereotype rooted in slavery.
"There is no way to excuse using a 'mammy' on our artwork, and so we have decided to remove it," they said in a statement. "We understand now that using a racist stereotype at all causes more damage than an explanation can repair, and we apologise. Moving forward, we will be donating a portion of our royalties from this record to the Equal Justice Initiative."
The experimental rockers also told fans they'd be reinstating "Here Comes the Indian" working title of "Ark".
"With utmost respect to Indigenous people we feel that having the word Indian in our record title sends the wrong message by objectifying the American Indian people which is not what we were intending with the music," they said.
"Because we have drawn countless inspiration from Indigenous people in America and around the world, moving forward, we will be donating a portion of our royalties from this record to Seeding Sovereignty, and changing the title to its original working title, Ark."