The scene first aired last year and was repeated on a DVD release in March. But in a particularly bad piece of timing for HBO, stories about it spread online this week, when the network premiered a documentary on Bush's father, former President George H.W. Bush.
Bush's head was one of several on spikes in a scene where King Joffrey reveals to his fiancé the severed head of her father, who he had judged disloyal.
The former president's features on the prosthetic head were partially obscured by long, scraggly hair and the picture flashes by quickly. But in a commentary included with the DVD, producers Dan Weiss and David Benioff pointed out the Bush head.
The producers said they often order prosthetic body parts in bulk for "Game of Thrones" because it can be too expensive to make new ones. It wasn't until the scene was shot that someone pointed out the resemblance to Bush, they said.
Their DVD commentary mentioning the Bush head made its presence clear to any fans who might not have noticed it the first time around.
"We meant no disrespect to the former president and apologize if anything we said or did suggested otherwise," the producers said in a statement.
HBO, in a statement issued by spokesman Quentin Schaffer, said it was dismayed to learn about the Bush head. "We find it unacceptable, disrespectful and in very bad taste," the network said.
HBO said it has halted all further shipments of the DVD and removed reruns of the episode from its networks until the scene with the severed Bush head is edited out.
The Associated Press contributed to this report.