He had guest Bret Weinstein, a former professor of evolutionary biology, with him on the show.
Both men are Covid vaccine sceptics who have lauded anti-parasitic drug ivermectin as a treatment for the virus, which the US Food and Drug Administration (FDA) strongly warns against.
Rogan said in the segment that the idea that he did not get vaccinated out of hate was “ridiculous” and went on to question the safety of the vaccine and criticise the US government.
On Thursday, Weinstein tweeted that the episode would be taken down temporarily “to address something we discovered after its release”.
“A tweet we discussed turns out not to be authentic, and there’s no way to preserve that part while protecting the person who was being impersonated,” he wrote.
On Friday, Rogan issued an apology.
“I was informed last night that this tweet is fake,” he wrote, retweeting a video of the segment.
“The show was already out, so we initially decided to post a notice saying we got tricked, then later thought it best to just delete it from the episode.
“My sincere apologies to everyone, especially the person who got hoaxed.”