The popular fantasy series is set in medieval times on another planet and follows several clans through a bloody struggle for ultimate power.
Season 1 of the show ended last year with numerous beheadings and a new king.
David Benioff and D.B. Weiss confirmed on the commentary for the DVD release of Season 1 that a prosthetic head bearing the likeness of Bush was among the noggins stuck on stakes and lining a castle wall.
"It's not a choice, not a political statement!" EW.com reported one of the writer-producers said during the commentary. "We just had to use what heads we had around."
HBO issued an apology in response to criticism from fans who said they felt the move was disrespectful.
"We were deeply dismayed to see this and find it unacceptable, disrespectful and in very bad taste. We made this clear to the executive producers of the series who apologized immediately for this inadvertent careless mistake. We are sorry this happened and will have it removed from any future DVD production," the cable network said.
EW.com said Benioff and Weiss released a separate statement, saying: "We use a lot of prosthetic body parts on the show: heads, arms, etc. We can't afford to have these all made from scratch, especially in scenes where we need a lot of them, so we rent them in bulk. After the scene was already shot, someone pointed out that one of the heads looked like George W. Bush. In the DVD commentary, we mentioned this, though we should not have. We meant no disrespect to the former president and apologize if anything we said or did suggested otherwise."