The actor confirmed in December the "sad news" he had been dropped, just months after announcing his return.
But Gunn, who recently took over the superhero franchise alongside Peter Safran, said on Tuesday that they didn't fire Cavill, but rather simply did not hire him for further projects.
BBC reports he made the comments while announcing a raft of new DC movies and TV shows.
"We didn't fire Henry," Gunn told journalists. "Henry was never cast.
"For me, it's about, who do I want to cast as Superman, and who do the filmmakers we have want to cast? And for me, for this story, it isn't Henry."
He added: "I like Henry, I think he's a great guy. I think he's getting [messed] around by a lot of people, including the former regime at this company. But this Superman is not Henry, for a number of reasons."
Cavill played Superman in films including Man Of Steel and Batman Vs Superman. Gunn and Safran took over DC Studios in October last year, just after Cavill had made a surprise appearance as the Man of Steel during the credits of the Dwayne Johnson film Black Adam.
The British star previously said there were no hard feelings though about the new DC co-chief executives opting to go in a new direction.
"After being told by the studio to announce my return back in October, prior to their hire, this news isn't the easiest, but that's life," Cavill said just before Christmas.