This follows a training accident yesterday - the second in as many months after a fatal crash in January.
Air force training group commander Group Captain Stephen Davies Howard confirmed the Red Checkers would not be at Wanaka this Easter (April 2-4) and would also be missing the Wild Foods Festival at Hokitika on Saturday week.
"It is a great shame, but it has not been a good year, " he said.
"But we've decided we need to work through the process of investigating the incident, and safety is always paramount when we are performing in public.
"We apologise to all of those who were looking forward to seeing the Red Checkers display this year."
The air force would, however, still be heavily involved in the airshow by sending a Tiger Moth, a Harvard, a C130 Hercules, a P3 Orion, two Iroquois helicopters and a Seasprite helicopter, he said.
Warbirds event manager Mandy Deans said the loss of the Red Checkers would be a "huge disappointment" as they were always a very popular attraction at the airshow.
Yesterday's incident, which occurred about 9.30am, resulted in a Red Checkers display aircraft suffering minor damage when it touched another aircraft during training, but the plane landed safely.
The incident came less than two months after Squadron Leader Nick Cree died when his aircraft crashed during training on January 15 near Bulls.
Grp Capt Davies Howard said there were always risks when planes flew in close proximity.
