Ganson was due to be the video referee for the clash between champions Leeds and leaders Wigan, which brings down the curtain on the two-day event at Manchester's Etihad Stadium.
However, the Rugby Football League announced a late change ahead of the opening game between Salford and Widnes, revealing that Ganson will be replaced by Ian Smith.
Ganson, who retired as an active referee two months ago to become the RFL's referees coach, blundered by awarding a try to Hull forward Chris Green even though slow-motion replays indicated that the player was offside.
The decision, which resulted in a 22-16 victory for Hull, was described by England international and reigning Man of Steel Sam Tomkins as the worst he had ever seen.
Furious Hull KR coach Craig Sandercock called on Ganson to make a public apology and it eventually came last night via Jon Sharp, the head of the RFL's match officials department.
"We have reviewed the decision and it is clear that Steve made the wrong call," Sharp said in a statement.
"Honesty and accountability are important to the match officials department and we can only apologise for the error.
"Steve has been in contact with Hull Kingston Rovers and offered his apologies. He is one of the sport's most experienced officials and deeply regrets having got it wrong.
"As with all fixtures, we will conduct a full review of the performance of our match officials following Magic Weekend and will take what steps we can to ensure that mistakes like this do not happen again."