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In February, it was reported that he had personally asked for 113 podcast episodes to be removed, including some featuring far-right commentators such as Alex Jones and Milo Yiannopoulos.
On this occasion, the missing episodes have been explained away by a “technical issue”.
“Spotify is aware of this technical issue, and we are looking into it now,” a company representative told the Los Angeles Times.
The Independent has reached out to a representative for Joe Rogan for comment.
The commentator signed a licensing deal to take his show and its back catalogue to Spotify in 2020. The agreement is rumoured to have been worth more than $200m (£160m).
The 36 newly removed episodes were reportedly recorded prior to Rogan’s exclusivity deal with the platform.
Earlier this month, the podcaster was heavily mocked online after realising he’d been discussing a fake news story while recording his podcast.
In the episode, released on 12 May, the commentator announced: “I read something briefly and I didn’t get into the article.” He then claimed that Australia is “trying to pass a bill that would outlaw you growing your own food”.
Believing the story to be true, Rogan mocked Australians for the fake proposed law, calling the lawmakers, which did not exist, “f***ing creeps” – before coming up short when trying to verify the story himself.
After a search failed to produce any results, he exclaimed to his guest: “Yep, I can’t find it either. Dammit! Better not be fake. It might be fake.”