Daniel Elk has sought to clarify the situation regarding the controversy surrounding the music streaming app's new policy allowing it to opt out of including musicians or songs it judges to be "harmful or hateful", which started with the 'Ignition (Remix)' hitmaker.
As reported by CNET, Elk spoke at Recode's Code Conference and said: "I think we rolled this out wrong and could have done a better job communicating it.
"The goal for this was to make sure we didn't have hate speech on the service; It was never about punishing one individual ... What we wanted to be was just transparent.
"If you are talking about being KKK and doing that kind of stuff, I think it's pretty obvious that we don't want you on the service."
A statement earlier this month revealed Spotify's new policy, and sparked claims of censorship within the app.
The statement read: "We are removing R. Kelly's music from all Spotify owned and operated playlists and algorithmic recommendations such as Discover Weekly.
"His music will still be available on the service, but Spotify will not actively promote it. We don't censor content because of an artist's or creator's behaviour, but we want our editorial decisions -- what we choose to program -- to reflect our values.
"When an artist or creator does something that is especially harmful or hateful, it may affect the ways we work with or support that artist or creator."
Spotify's removal of the rapper - whose real name is Robert Sylvester Kelly - from their playlists comes after a number of sexual assault allegations have been made against him over the years, which prompted a group of women to start the #MuteRKelly campaign on social media.
Kelly, 51, has strongly denied all claims made against him, and has released the following statement regarding Spotify's decision to Metro.co.uk: "My team has advised me that this is not a proper platform to express my emotions. I will not discuss details about these false allegations that have been made against me."