In a post Monday, the 38-year-old actor and comedian clarified his remarks about working with Watson, 30, on the 2013 movie.
In an interview with British GQ published Monday, Rogen appeared to confirm a rumor that Watson "stormed off the set" of This is the End after refusing to shoot a scene where Danny McBride played a cannibal.
"I mean, I don't look back on that and think, 'How dare she do that?' You know? I think sometimes when you read something, when it comes to life it doesn't seem to be what you thought it was," Rogen told British GQ.
"But it was not some terrible ending to our relationship. She came back the next day to say goodbye. She helped promote the film," he said. "No hard feelings and I couldn't be happier with how the film turned out in the end."
In his post Monday, Rogen apologized for putting Watson in an "uncomfortable position."
"I want to correct a story that has emerged from a recent interview I gave. It misrepresents what actually happened. Emma Watson did not 'storm off the set' and it's [expletive] that the perception is that she did," the actor said.
"The scene was not what was originally scripted, it was getting improvised, changed drastically and was not what she agreed to. The narrative that she was in some way uncool or unprofessional is complete [expletive]," he added.
Rogen said he's happy Watson spoke up and hopes to work with the actress again in the future.
"I for sure should have communicated better and because I didn't, she was put in an uncomfortable position," Rogen said. "She and I spoke on the night; it was overall a [expletive] situation and it must have been hard for her to say something and I'm very happy and impressed that she did. We agreed on her not being in the scene together."
"I was thrilled for the opportunity to work with her and would be thrilled to get that opportunity again. I am very sorry and disappointed it happened, and I wish I had done more to prevent it," he concluded.
Rogen wrote, directed, produced and starred in This is the End, a comedy that takes place in the wake of a global apocalypse. The movie co-stars James Franco, Craig Robinson, Jay Baruchel, Jonah Hill, Danny McBride and Michael Cera.