"We regret Neil's decision to remove his music from Spotify," the company said in a statement, according to the Associated Press.
"But we hope to welcome him back soon."
In his podcast, Joe Rogan has, among other things, questioned the benefit of mass vaccination against the coronavirus.
Since 2020, Spotify has exclusive rights to the podcast after a deal of SEK 900 million.
Clear content rules
Spotify says that it has clear content rules and that 20,000 podcast episodes related to covid-19 have been removed during the pandemic.
Neil Young came out with his criticism in an open letter earlier this week.
”Jag gör det här för att Spotify sprider falsk information om vaccin och potentiellt orsakar dödsfall bland dem som tror på desinformationen som sprids”, skrev han.
Under natten mot torsdagen gick det fortfarande att lyssna på stjärnans låtar på Spotify i Sverige.